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smdabdoub/phylotoast
|
phylotoast/util.py
|
split_phylogeny
|
def split_phylogeny(p, level="s"):
"""
Return either the full or truncated version of a QIIME-formatted taxonomy string.
:type p: str
:param p: A QIIME-formatted taxonomy string: k__Foo; p__Bar; ...
:type level: str
:param level: The different level of identification are kingdom (k), phylum (p),
class (c),order (o), family (f), genus (g) and species (s). If level is
not provided, the default level of identification is species.
:rtype: str
:return: A QIIME-formatted taxonomy string up to the classification given
by param level.
"""
level = level+"__"
result = p.split(level)
return result[0]+level+result[1].split(";")[0]
|
python
|
def split_phylogeny(p, level="s"):
"""
Return either the full or truncated version of a QIIME-formatted taxonomy string.
:type p: str
:param p: A QIIME-formatted taxonomy string: k__Foo; p__Bar; ...
:type level: str
:param level: The different level of identification are kingdom (k), phylum (p),
class (c),order (o), family (f), genus (g) and species (s). If level is
not provided, the default level of identification is species.
:rtype: str
:return: A QIIME-formatted taxonomy string up to the classification given
by param level.
"""
level = level+"__"
result = p.split(level)
return result[0]+level+result[1].split(";")[0]
|
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Return either the full or truncated version of a QIIME-formatted taxonomy string.
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:param p: A QIIME-formatted taxonomy string: k__Foo; p__Bar; ...
:type level: str
:param level: The different level of identification are kingdom (k), phylum (p),
class (c),order (o), family (f), genus (g) and species (s). If level is
not provided, the default level of identification is species.
:rtype: str
:return: A QIIME-formatted taxonomy string up to the classification given
by param level.
|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L159-L177
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
ensure_dir
|
def ensure_dir(d):
"""
Check to make sure the supplied directory path does not exist, if so, create it. The
method catches OSError exceptions and returns a descriptive message instead of
re-raising the error.
:type d: str
:param d: It is the full path to a directory.
:return: Does not return anything, but creates a directory path if it doesn't exist
already.
"""
if not os.path.exists(d):
try:
os.makedirs(d)
except OSError as oe:
# should not happen with os.makedirs
# ENOENT: No such file or directory
if os.errno == errno.ENOENT:
msg = twdd("""One or more directories in the path ({}) do not exist. If
you are specifying a new directory for output, please ensure
all other directories in the path currently exist.""")
return msg.format(d)
else:
msg = twdd("""An error occurred trying to create the output directory
({}) with message: {}""")
return msg.format(d, oe.strerror)
|
python
|
def ensure_dir(d):
"""
Check to make sure the supplied directory path does not exist, if so, create it. The
method catches OSError exceptions and returns a descriptive message instead of
re-raising the error.
:type d: str
:param d: It is the full path to a directory.
:return: Does not return anything, but creates a directory path if it doesn't exist
already.
"""
if not os.path.exists(d):
try:
os.makedirs(d)
except OSError as oe:
# should not happen with os.makedirs
# ENOENT: No such file or directory
if os.errno == errno.ENOENT:
msg = twdd("""One or more directories in the path ({}) do not exist. If
you are specifying a new directory for output, please ensure
all other directories in the path currently exist.""")
return msg.format(d)
else:
msg = twdd("""An error occurred trying to create the output directory
({}) with message: {}""")
return msg.format(d, oe.strerror)
|
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|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L180-L206
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
file_handle
|
def file_handle(fnh, mode="rU"):
"""
Takes either a file path or an open file handle, checks validity and returns an open
file handle or raises an appropriate Exception.
:type fnh: str
:param fnh: It is the full path to a file, or open file handle
:type mode: str
:param mode: The way in which this file will be used, for example to read or write or
both. By default, file will be opened in rU mode.
:return: Returns an opened file for appropriate usage.
"""
handle = None
if isinstance(fnh, file):
if fnh.closed:
raise ValueError("Input file is closed.")
handle = fnh
elif isinstance(fnh, str):
handle = open(fnh, mode)
return handle
|
python
|
def file_handle(fnh, mode="rU"):
"""
Takes either a file path or an open file handle, checks validity and returns an open
file handle or raises an appropriate Exception.
:type fnh: str
:param fnh: It is the full path to a file, or open file handle
:type mode: str
:param mode: The way in which this file will be used, for example to read or write or
both. By default, file will be opened in rU mode.
:return: Returns an opened file for appropriate usage.
"""
handle = None
if isinstance(fnh, file):
if fnh.closed:
raise ValueError("Input file is closed.")
handle = fnh
elif isinstance(fnh, str):
handle = open(fnh, mode)
return handle
|
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|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L209-L231
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
gather_categories
|
def gather_categories(imap, header, categories=None):
"""
Find the user specified categories in the map and create a dictionary to contain the
relevant data for each type within the categories. Multiple categories will have their
types combined such that each possible combination will have its own entry in the
dictionary.
:type imap: dict
:param imap: The input mapping file data keyed by SampleID
:type header: list
:param header: The header line from the input mapping file. This will be searched for
the user-specified categories
:type categories: list
:param categories: The list of user-specified category column name from mapping file
:rtype: dict
:return: A sorted dictionary keyed on the combinations of all the types found within
the user-specified categories. Each entry will contain an empty DataCategory
namedtuple. If no categories are specified, a single entry with the key
'default' will be returned
"""
# If no categories provided, return all SampleIDs
if categories is None:
return {"default": DataCategory(set(imap.keys()), {})}
cat_ids = [header.index(cat)
for cat in categories if cat in header and "=" not in cat]
table = OrderedDict()
conditions = defaultdict(set)
for i, cat in enumerate(categories):
if "=" in cat and cat.split("=")[0] in header:
cat_name = header[header.index(cat.split("=")[0])]
conditions[cat_name].add(cat.split("=")[1])
# If invalid categories or conditions identified, return all SampleIDs
if not cat_ids and not conditions:
return {"default": DataCategory(set(imap.keys()), {})}
#If only category column given, return column-wise SampleIDs
if cat_ids and not conditions:
for sid, row in imap.items():
cat_name = "_".join([row[cid] for cid in cat_ids])
if cat_name not in table:
table[cat_name] = DataCategory(set(), {})
table[cat_name].sids.add(sid)
return table
# Collect all condition names
cond_ids = set()
for k in conditions:
try:
cond_ids.add(header.index(k))
except ValueError:
continue
idx_to_test = set(cat_ids).union(cond_ids)
# If column name and condition given, return overlapping SampleIDs of column and
# condition combinations
for sid, row in imap.items():
if all([row[header.index(c)] in conditions[c] for c in conditions]):
key = "_".join([row[idx] for idx in idx_to_test])
try:
assert key in table.keys()
except AssertionError:
table[key] = DataCategory(set(), {})
table[key].sids.add(sid)
try:
assert len(table) > 0
except AssertionError:
return {"default": DataCategory(set(imap.keys()), {})}
else:
return table
|
python
|
def gather_categories(imap, header, categories=None):
"""
Find the user specified categories in the map and create a dictionary to contain the
relevant data for each type within the categories. Multiple categories will have their
types combined such that each possible combination will have its own entry in the
dictionary.
:type imap: dict
:param imap: The input mapping file data keyed by SampleID
:type header: list
:param header: The header line from the input mapping file. This will be searched for
the user-specified categories
:type categories: list
:param categories: The list of user-specified category column name from mapping file
:rtype: dict
:return: A sorted dictionary keyed on the combinations of all the types found within
the user-specified categories. Each entry will contain an empty DataCategory
namedtuple. If no categories are specified, a single entry with the key
'default' will be returned
"""
# If no categories provided, return all SampleIDs
if categories is None:
return {"default": DataCategory(set(imap.keys()), {})}
cat_ids = [header.index(cat)
for cat in categories if cat in header and "=" not in cat]
table = OrderedDict()
conditions = defaultdict(set)
for i, cat in enumerate(categories):
if "=" in cat and cat.split("=")[0] in header:
cat_name = header[header.index(cat.split("=")[0])]
conditions[cat_name].add(cat.split("=")[1])
# If invalid categories or conditions identified, return all SampleIDs
if not cat_ids and not conditions:
return {"default": DataCategory(set(imap.keys()), {})}
#If only category column given, return column-wise SampleIDs
if cat_ids and not conditions:
for sid, row in imap.items():
cat_name = "_".join([row[cid] for cid in cat_ids])
if cat_name not in table:
table[cat_name] = DataCategory(set(), {})
table[cat_name].sids.add(sid)
return table
# Collect all condition names
cond_ids = set()
for k in conditions:
try:
cond_ids.add(header.index(k))
except ValueError:
continue
idx_to_test = set(cat_ids).union(cond_ids)
# If column name and condition given, return overlapping SampleIDs of column and
# condition combinations
for sid, row in imap.items():
if all([row[header.index(c)] in conditions[c] for c in conditions]):
key = "_".join([row[idx] for idx in idx_to_test])
try:
assert key in table.keys()
except AssertionError:
table[key] = DataCategory(set(), {})
table[key].sids.add(sid)
try:
assert len(table) > 0
except AssertionError:
return {"default": DataCategory(set(imap.keys()), {})}
else:
return table
|
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:param imap: The input mapping file data keyed by SampleID
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the user-specified categories
:type categories: list
:param categories: The list of user-specified category column name from mapping file
:rtype: dict
:return: A sorted dictionary keyed on the combinations of all the types found within
the user-specified categories. Each entry will contain an empty DataCategory
namedtuple. If no categories are specified, a single entry with the key
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|
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0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L238-L309
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
parse_unifrac
|
def parse_unifrac(unifracFN):
"""
Parses the unifrac results file into a dictionary
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:rtype: dict
:return: A dictionary with keys: 'pcd' (principle coordinates data) which is a
dictionary of the data keyed by sample ID, 'eigvals' (eigenvalues), and
'varexp' (variation explained)
"""
with open(unifracFN, "rU") as uF:
first = uF.next().split("\t")
lines = [line.strip() for line in uF]
unifrac = {"pcd": OrderedDict(), "eigvals": [], "varexp": []}
if first[0] == "pc vector number":
return parse_unifrac_v1_8(unifrac, lines)
elif first[0] == "Eigvals":
return parse_unifrac_v1_9(unifrac, lines)
else:
raise ValueError("File format not supported/recognized. Please check input "
"unifrac file.")
|
python
|
def parse_unifrac(unifracFN):
"""
Parses the unifrac results file into a dictionary
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:rtype: dict
:return: A dictionary with keys: 'pcd' (principle coordinates data) which is a
dictionary of the data keyed by sample ID, 'eigvals' (eigenvalues), and
'varexp' (variation explained)
"""
with open(unifracFN, "rU") as uF:
first = uF.next().split("\t")
lines = [line.strip() for line in uF]
unifrac = {"pcd": OrderedDict(), "eigvals": [], "varexp": []}
if first[0] == "pc vector number":
return parse_unifrac_v1_8(unifrac, lines)
elif first[0] == "Eigvals":
return parse_unifrac_v1_9(unifrac, lines)
else:
raise ValueError("File format not supported/recognized. Please check input "
"unifrac file.")
|
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Parses the unifrac results file into a dictionary
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:rtype: dict
:return: A dictionary with keys: 'pcd' (principle coordinates data) which is a
dictionary of the data keyed by sample ID, 'eigvals' (eigenvalues), and
'varexp' (variation explained)
|
[
"Parses",
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L311-L334
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
parse_unifrac_v1_8
|
def parse_unifrac_v1_8(unifrac, file_data):
"""
Function to parse data from older version of unifrac file obtained from Qiime version
1.8 and earlier.
:type unifrac: dict
:param unifracFN: The path to the unifrac results file
:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
"""
for line in file_data:
if line == "":
break
line = line.split("\t")
unifrac["pcd"][line[0]] = [float(e) for e in line[1:]]
unifrac["eigvals"] = [float(entry) for entry in file_data[-2].split("\t")[1:]]
unifrac["varexp"] = [float(entry) for entry in file_data[-1].split("\t")[1:]]
return unifrac
|
python
|
def parse_unifrac_v1_8(unifrac, file_data):
"""
Function to parse data from older version of unifrac file obtained from Qiime version
1.8 and earlier.
:type unifrac: dict
:param unifracFN: The path to the unifrac results file
:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
"""
for line in file_data:
if line == "":
break
line = line.split("\t")
unifrac["pcd"][line[0]] = [float(e) for e in line[1:]]
unifrac["eigvals"] = [float(entry) for entry in file_data[-2].split("\t")[1:]]
unifrac["varexp"] = [float(entry) for entry in file_data[-1].split("\t")[1:]]
return unifrac
|
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Function to parse data from older version of unifrac file obtained from Qiime version
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:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
|
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0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L337-L356
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
parse_unifrac_v1_9
|
def parse_unifrac_v1_9(unifrac, file_data):
"""
Function to parse data from newer version of unifrac file obtained from Qiime version
1.9 and later.
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
"""
unifrac["eigvals"] = [float(entry) for entry in file_data[0].split("\t")]
unifrac["varexp"] = [float(entry)*100 for entry in file_data[3].split("\t")]
for line in file_data[8:]:
if line == "":
break
line = line.split("\t")
unifrac["pcd"][line[0]] = [float(e) for e in line[1:]]
return unifrac
|
python
|
def parse_unifrac_v1_9(unifrac, file_data):
"""
Function to parse data from newer version of unifrac file obtained from Qiime version
1.9 and later.
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
"""
unifrac["eigvals"] = [float(entry) for entry in file_data[0].split("\t")]
unifrac["varexp"] = [float(entry)*100 for entry in file_data[3].split("\t")]
for line in file_data[8:]:
if line == "":
break
line = line.split("\t")
unifrac["pcd"][line[0]] = [float(e) for e in line[1:]]
return unifrac
|
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Function to parse data from newer version of unifrac file obtained from Qiime version
1.9 and later.
:type unifracFN: str
:param unifracFN: The path to the unifrac results file
:type file_data: list
:param file_data: Unifrac data lines after stripping whitespace characters.
|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L359-L378
|
train
|
smdabdoub/phylotoast
|
phylotoast/util.py
|
color_mapping
|
def color_mapping(sample_map, header, group_column, color_column=None):
"""
Determine color-category mapping. If color_column was specified, then map the category
names to color values. Otherwise, use the palettable colors to automatically generate
a set of colors for the group values.
:type sample_map: dict
:param unifracFN: Map associating each line of the mapping file with the appropriate
sample ID (each value of the map also contains the sample ID)
:type header: tuple
:param A tuple of header line for mapping file
:type group_column: str
:param group_column: String denoting the column name for sample groups.
:type color_column: str
:param color_column: String denoting the column name for sample colors.
:type return: dict
:param return: {SampleID: Color}
"""
group_colors = OrderedDict()
group_gather = gather_categories(sample_map, header, [group_column])
if color_column is not None:
color_gather = gather_categories(sample_map, header, [color_column])
# match sample IDs between color_gather and group_gather
for group in group_gather:
for color in color_gather:
# allow incomplete assignment of colors, if group sids overlap at
# all with the color sids, consider it a match
if group_gather[group].sids.intersection(color_gather[color].sids):
group_colors[group] = color
else:
bcolors = itertools.cycle(Set3_12.hex_colors)
for group in group_gather:
group_colors[group] = bcolors.next()
return group_colors
|
python
|
def color_mapping(sample_map, header, group_column, color_column=None):
"""
Determine color-category mapping. If color_column was specified, then map the category
names to color values. Otherwise, use the palettable colors to automatically generate
a set of colors for the group values.
:type sample_map: dict
:param unifracFN: Map associating each line of the mapping file with the appropriate
sample ID (each value of the map also contains the sample ID)
:type header: tuple
:param A tuple of header line for mapping file
:type group_column: str
:param group_column: String denoting the column name for sample groups.
:type color_column: str
:param color_column: String denoting the column name for sample colors.
:type return: dict
:param return: {SampleID: Color}
"""
group_colors = OrderedDict()
group_gather = gather_categories(sample_map, header, [group_column])
if color_column is not None:
color_gather = gather_categories(sample_map, header, [color_column])
# match sample IDs between color_gather and group_gather
for group in group_gather:
for color in color_gather:
# allow incomplete assignment of colors, if group sids overlap at
# all with the color sids, consider it a match
if group_gather[group].sids.intersection(color_gather[color].sids):
group_colors[group] = color
else:
bcolors = itertools.cycle(Set3_12.hex_colors)
for group in group_gather:
group_colors[group] = bcolors.next()
return group_colors
|
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Determine color-category mapping. If color_column was specified, then map the category
names to color values. Otherwise, use the palettable colors to automatically generate
a set of colors for the group values.
:type sample_map: dict
:param unifracFN: Map associating each line of the mapping file with the appropriate
sample ID (each value of the map also contains the sample ID)
:type header: tuple
:param A tuple of header line for mapping file
:type group_column: str
:param group_column: String denoting the column name for sample groups.
:type color_column: str
:param color_column: String denoting the column name for sample colors.
:type return: dict
:param return: {SampleID: Color}
|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L380-L419
|
train
|
christophertbrown/bioscripts
|
ctbBio/shuffle_genome.py
|
rev_c
|
def rev_c(read):
"""
return reverse completment of read
"""
rc = []
rc_nucs = {'A':'T', 'T':'A', 'G':'C', 'C':'G', 'N':'N'}
for base in read:
rc.extend(rc_nucs[base.upper()])
return rc[::-1]
|
python
|
def rev_c(read):
"""
return reverse completment of read
"""
rc = []
rc_nucs = {'A':'T', 'T':'A', 'G':'C', 'C':'G', 'N':'N'}
for base in read:
rc.extend(rc_nucs[base.upper()])
return rc[::-1]
|
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return reverse completment of read
|
[
"return",
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"of",
"read"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/shuffle_genome.py#L27-L35
|
train
|
christophertbrown/bioscripts
|
ctbBio/shuffle_genome.py
|
shuffle_genome
|
def shuffle_genome(genome, cat, fraction = float(100), plot = True, \
alpha = 0.1, beta = 100000, \
min_length = 1000, max_length = 200000):
"""
randomly shuffle genome
"""
header = '>randomized_%s' % (genome.name)
sequence = list(''.join([i[1] for i in parse_fasta(genome)]))
length = len(sequence)
shuffled = []
# break genome into pieces
while sequence is not False:
s = int(random.gammavariate(alpha, beta))
if s <= min_length or s >= max_length:
continue
if len(sequence) < s:
seq = sequence[0:]
else:
seq = sequence[0:s]
sequence = sequence[s:]
# if bool(random.getrandbits(1)) is True:
# seq = rev_c(seq)
# print('fragment length: %s reverse complement: True' % ('{:,}'.format(s)), file=sys.stderr)
# else:
# print('fragment length: %s reverse complement: False' % ('{:,}'.format(s)), file=sys.stderr)
shuffled.append(''.join(seq))
if sequence == []:
break
# shuffle pieces
random.shuffle(shuffled)
# subset fragments
if fraction == float(100):
subset = shuffled
else:
max_pieces = int(length * fraction/100)
subset, total = [], 0
for fragment in shuffled:
length = len(fragment)
if total + length <= max_pieces:
subset.append(fragment)
total += length
else:
diff = max_pieces - total
subset.append(fragment[0:diff])
break
# combine sequences, if requested
if cat is True:
yield [header, ''.join(subset)]
else:
for i, seq in enumerate(subset):
yield ['%s fragment:%s' % (header, i), seq]
|
python
|
def shuffle_genome(genome, cat, fraction = float(100), plot = True, \
alpha = 0.1, beta = 100000, \
min_length = 1000, max_length = 200000):
"""
randomly shuffle genome
"""
header = '>randomized_%s' % (genome.name)
sequence = list(''.join([i[1] for i in parse_fasta(genome)]))
length = len(sequence)
shuffled = []
# break genome into pieces
while sequence is not False:
s = int(random.gammavariate(alpha, beta))
if s <= min_length or s >= max_length:
continue
if len(sequence) < s:
seq = sequence[0:]
else:
seq = sequence[0:s]
sequence = sequence[s:]
# if bool(random.getrandbits(1)) is True:
# seq = rev_c(seq)
# print('fragment length: %s reverse complement: True' % ('{:,}'.format(s)), file=sys.stderr)
# else:
# print('fragment length: %s reverse complement: False' % ('{:,}'.format(s)), file=sys.stderr)
shuffled.append(''.join(seq))
if sequence == []:
break
# shuffle pieces
random.shuffle(shuffled)
# subset fragments
if fraction == float(100):
subset = shuffled
else:
max_pieces = int(length * fraction/100)
subset, total = [], 0
for fragment in shuffled:
length = len(fragment)
if total + length <= max_pieces:
subset.append(fragment)
total += length
else:
diff = max_pieces - total
subset.append(fragment[0:diff])
break
# combine sequences, if requested
if cat is True:
yield [header, ''.join(subset)]
else:
for i, seq in enumerate(subset):
yield ['%s fragment:%s' % (header, i), seq]
|
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randomly shuffle genome
|
[
"randomly",
"shuffle",
"genome"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/shuffle_genome.py#L37-L87
|
train
|
opengridcc/opengrid
|
opengrid/library/regression.py
|
MultiVarLinReg._prune
|
def _prune(self, fit, p_max):
"""
If the fit contains statistically insignificant parameters, remove them.
Returns a pruned fit where all parameters have p-values of the t-statistic below p_max
Parameters
----------
fit: fm.ols fit object
Can contain insignificant parameters
p_max : float
Maximum allowed probability of the t-statistic
Returns
-------
fit: fm.ols fit object
Won't contain any insignificant parameters
"""
def remove_from_model_desc(x, model_desc):
"""
Return a model_desc without x
"""
rhs_termlist = []
for t in model_desc.rhs_termlist:
if not t.factors:
# intercept, add anyway
rhs_termlist.append(t)
elif not x == t.factors[0]._varname:
# this is not the term with x
rhs_termlist.append(t)
md = ModelDesc(model_desc.lhs_termlist, rhs_termlist)
return md
corrected_model_desc = ModelDesc(fit.model.formula.lhs_termlist[:], fit.model.formula.rhs_termlist[:])
pars_to_prune = fit.pvalues.where(fit.pvalues > p_max).dropna().index.tolist()
try:
pars_to_prune.remove('Intercept')
except:
pass
while pars_to_prune:
corrected_model_desc = remove_from_model_desc(pars_to_prune[0], corrected_model_desc)
fit = fm.ols(corrected_model_desc, data=self.df).fit()
pars_to_prune = fit.pvalues.where(fit.pvalues > p_max).dropna().index.tolist()
try:
pars_to_prune.remove('Intercept')
except:
pass
return fit
|
python
|
def _prune(self, fit, p_max):
"""
If the fit contains statistically insignificant parameters, remove them.
Returns a pruned fit where all parameters have p-values of the t-statistic below p_max
Parameters
----------
fit: fm.ols fit object
Can contain insignificant parameters
p_max : float
Maximum allowed probability of the t-statistic
Returns
-------
fit: fm.ols fit object
Won't contain any insignificant parameters
"""
def remove_from_model_desc(x, model_desc):
"""
Return a model_desc without x
"""
rhs_termlist = []
for t in model_desc.rhs_termlist:
if not t.factors:
# intercept, add anyway
rhs_termlist.append(t)
elif not x == t.factors[0]._varname:
# this is not the term with x
rhs_termlist.append(t)
md = ModelDesc(model_desc.lhs_termlist, rhs_termlist)
return md
corrected_model_desc = ModelDesc(fit.model.formula.lhs_termlist[:], fit.model.formula.rhs_termlist[:])
pars_to_prune = fit.pvalues.where(fit.pvalues > p_max).dropna().index.tolist()
try:
pars_to_prune.remove('Intercept')
except:
pass
while pars_to_prune:
corrected_model_desc = remove_from_model_desc(pars_to_prune[0], corrected_model_desc)
fit = fm.ols(corrected_model_desc, data=self.df).fit()
pars_to_prune = fit.pvalues.where(fit.pvalues > p_max).dropna().index.tolist()
try:
pars_to_prune.remove('Intercept')
except:
pass
return fit
|
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Can contain insignificant parameters
p_max : float
Maximum allowed probability of the t-statistic
Returns
-------
fit: fm.ols fit object
Won't contain any insignificant parameters
|
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69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L222-L272
|
train
|
opengridcc/opengrid
|
opengrid/library/regression.py
|
MultiVarLinReg.find_best_rsquared
|
def find_best_rsquared(list_of_fits):
"""Return the best fit, based on rsquared"""
res = sorted(list_of_fits, key=lambda x: x.rsquared)
return res[-1]
|
python
|
def find_best_rsquared(list_of_fits):
"""Return the best fit, based on rsquared"""
res = sorted(list_of_fits, key=lambda x: x.rsquared)
return res[-1]
|
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Return the best fit, based on rsquared
|
[
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69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L275-L278
|
train
|
opengridcc/opengrid
|
opengrid/library/regression.py
|
MultiVarLinReg._predict
|
def _predict(self, fit, df):
"""
Return a df with predictions and confidence interval
Notes
-----
The df will contain the following columns:
- 'predicted': the model output
- 'interval_u', 'interval_l': upper and lower confidence bounds.
The result will depend on the following attributes of self:
confint : float (default=0.95)
Confidence level for two-sided hypothesis
allow_negative_predictions : bool (default=True)
If False, correct negative predictions to zero (typically for energy consumption predictions)
Parameters
----------
fit : Statsmodels fit
df : pandas DataFrame or None (default)
If None, use self.df
Returns
-------
df_res : pandas DataFrame
Copy of df with additional columns 'predicted', 'interval_u' and 'interval_l'
"""
# Add model results to data as column 'predictions'
df_res = df.copy()
if 'Intercept' in fit.model.exog_names:
df_res['Intercept'] = 1.0
df_res['predicted'] = fit.predict(df_res)
if not self.allow_negative_predictions:
df_res.loc[df_res['predicted'] < 0, 'predicted'] = 0
prstd, interval_l, interval_u = wls_prediction_std(fit,
df_res[fit.model.exog_names],
alpha=1 - self.confint)
df_res['interval_l'] = interval_l
df_res['interval_u'] = interval_u
if 'Intercept' in df_res:
df_res.drop(labels=['Intercept'], axis=1, inplace=True)
return df_res
|
python
|
def _predict(self, fit, df):
"""
Return a df with predictions and confidence interval
Notes
-----
The df will contain the following columns:
- 'predicted': the model output
- 'interval_u', 'interval_l': upper and lower confidence bounds.
The result will depend on the following attributes of self:
confint : float (default=0.95)
Confidence level for two-sided hypothesis
allow_negative_predictions : bool (default=True)
If False, correct negative predictions to zero (typically for energy consumption predictions)
Parameters
----------
fit : Statsmodels fit
df : pandas DataFrame or None (default)
If None, use self.df
Returns
-------
df_res : pandas DataFrame
Copy of df with additional columns 'predicted', 'interval_u' and 'interval_l'
"""
# Add model results to data as column 'predictions'
df_res = df.copy()
if 'Intercept' in fit.model.exog_names:
df_res['Intercept'] = 1.0
df_res['predicted'] = fit.predict(df_res)
if not self.allow_negative_predictions:
df_res.loc[df_res['predicted'] < 0, 'predicted'] = 0
prstd, interval_l, interval_u = wls_prediction_std(fit,
df_res[fit.model.exog_names],
alpha=1 - self.confint)
df_res['interval_l'] = interval_l
df_res['interval_u'] = interval_u
if 'Intercept' in df_res:
df_res.drop(labels=['Intercept'], axis=1, inplace=True)
return df_res
|
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The result will depend on the following attributes of self:
confint : float (default=0.95)
Confidence level for two-sided hypothesis
allow_negative_predictions : bool (default=True)
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Parameters
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fit : Statsmodels fit
df : pandas DataFrame or None (default)
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69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L292-L338
|
train
|
smdabdoub/phylotoast
|
phylotoast/biom_calc.py
|
relative_abundance
|
def relative_abundance(biomf, sampleIDs=None):
"""
Calculate the relative abundance of each OTUID in a Sample.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: list
:param sampleIDs: A list of sample id's from BIOM format OTU table.
:rtype: dict
:return: Returns a keyed on SampleIDs, and the values are dictionaries keyed on
OTUID's and their values represent the relative abundance of that OTUID in
that SampleID.
"""
if sampleIDs is None:
sampleIDs = biomf.ids()
else:
try:
for sid in sampleIDs:
assert sid in biomf.ids()
except AssertionError:
raise ValueError(
"\nError while calculating relative abundances: The sampleIDs provided do"
" not match the sampleIDs in biom file. Please double check the sampleIDs"
" provided.\n")
otuIDs = biomf.ids(axis="observation")
norm_biomf = biomf.norm(inplace=False)
return {sample: {otuID: norm_biomf.get_value_by_ids(otuID, sample)
for otuID in otuIDs} for sample in sampleIDs}
|
python
|
def relative_abundance(biomf, sampleIDs=None):
"""
Calculate the relative abundance of each OTUID in a Sample.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: list
:param sampleIDs: A list of sample id's from BIOM format OTU table.
:rtype: dict
:return: Returns a keyed on SampleIDs, and the values are dictionaries keyed on
OTUID's and their values represent the relative abundance of that OTUID in
that SampleID.
"""
if sampleIDs is None:
sampleIDs = biomf.ids()
else:
try:
for sid in sampleIDs:
assert sid in biomf.ids()
except AssertionError:
raise ValueError(
"\nError while calculating relative abundances: The sampleIDs provided do"
" not match the sampleIDs in biom file. Please double check the sampleIDs"
" provided.\n")
otuIDs = biomf.ids(axis="observation")
norm_biomf = biomf.norm(inplace=False)
return {sample: {otuID: norm_biomf.get_value_by_ids(otuID, sample)
for otuID in otuIDs} for sample in sampleIDs}
|
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Calculate the relative abundance of each OTUID in a Sample.
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0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L11-L41
|
train
|
smdabdoub/phylotoast
|
phylotoast/biom_calc.py
|
mean_otu_pct_abundance
|
def mean_otu_pct_abundance(ra, otuIDs):
"""
Calculate the mean OTU abundance percentage.
:type ra: Dict
:param ra: 'ra' refers to a dictionary keyed on SampleIDs, and the values are
dictionaries keyed on OTUID's and their values represent the relative
abundance of that OTUID in that SampleID. 'ra' is the output of
relative_abundance() function.
:type otuIDs: List
:param otuIDs: A list of OTUID's for which the percentage abundance needs to be
measured.
:rtype: dict
:return: A dictionary of OTUID and their percent relative abundance as key/value pair.
"""
sids = ra.keys()
otumeans = defaultdict(int)
for oid in otuIDs:
otumeans[oid] = sum([ra[sid][oid] for sid in sids
if oid in ra[sid]]) / len(sids) * 100
return otumeans
|
python
|
def mean_otu_pct_abundance(ra, otuIDs):
"""
Calculate the mean OTU abundance percentage.
:type ra: Dict
:param ra: 'ra' refers to a dictionary keyed on SampleIDs, and the values are
dictionaries keyed on OTUID's and their values represent the relative
abundance of that OTUID in that SampleID. 'ra' is the output of
relative_abundance() function.
:type otuIDs: List
:param otuIDs: A list of OTUID's for which the percentage abundance needs to be
measured.
:rtype: dict
:return: A dictionary of OTUID and their percent relative abundance as key/value pair.
"""
sids = ra.keys()
otumeans = defaultdict(int)
for oid in otuIDs:
otumeans[oid] = sum([ra[sid][oid] for sid in sids
if oid in ra[sid]]) / len(sids) * 100
return otumeans
|
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")",
"*",
"100",
"return",
"otumeans"
] |
Calculate the mean OTU abundance percentage.
:type ra: Dict
:param ra: 'ra' refers to a dictionary keyed on SampleIDs, and the values are
dictionaries keyed on OTUID's and their values represent the relative
abundance of that OTUID in that SampleID. 'ra' is the output of
relative_abundance() function.
:type otuIDs: List
:param otuIDs: A list of OTUID's for which the percentage abundance needs to be
measured.
:rtype: dict
:return: A dictionary of OTUID and their percent relative abundance as key/value pair.
|
[
"Calculate",
"the",
"mean",
"OTU",
"abundance",
"percentage",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L44-L67
|
train
|
smdabdoub/phylotoast
|
phylotoast/biom_calc.py
|
MRA
|
def MRA(biomf, sampleIDs=None, transform=None):
"""
Calculate the mean relative abundance percentage.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: list
:param sampleIDs: A list of sample id's from BIOM format OTU table.
:param transform: Mathematical function which is used to transform smax to another
format. By default, the function has been set to None.
:rtype: dict
:return: A dictionary keyed on OTUID's and their mean relative abundance for a given
number of sampleIDs.
"""
ra = relative_abundance(biomf, sampleIDs)
if transform is not None:
ra = {sample: {otuID: transform(abd) for otuID, abd in ra[sample].items()}
for sample in ra.keys()}
otuIDs = biomf.ids(axis="observation")
return mean_otu_pct_abundance(ra, otuIDs)
|
python
|
def MRA(biomf, sampleIDs=None, transform=None):
"""
Calculate the mean relative abundance percentage.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: list
:param sampleIDs: A list of sample id's from BIOM format OTU table.
:param transform: Mathematical function which is used to transform smax to another
format. By default, the function has been set to None.
:rtype: dict
:return: A dictionary keyed on OTUID's and their mean relative abundance for a given
number of sampleIDs.
"""
ra = relative_abundance(biomf, sampleIDs)
if transform is not None:
ra = {sample: {otuID: transform(abd) for otuID, abd in ra[sample].items()}
for sample in ra.keys()}
otuIDs = biomf.ids(axis="observation")
return mean_otu_pct_abundance(ra, otuIDs)
|
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Calculate the mean relative abundance percentage.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: list
:param sampleIDs: A list of sample id's from BIOM format OTU table.
:param transform: Mathematical function which is used to transform smax to another
format. By default, the function has been set to None.
:rtype: dict
:return: A dictionary keyed on OTUID's and their mean relative abundance for a given
number of sampleIDs.
|
[
"Calculate",
"the",
"mean",
"relative",
"abundance",
"percentage",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L70-L92
|
train
|
smdabdoub/phylotoast
|
phylotoast/biom_calc.py
|
raw_abundance
|
def raw_abundance(biomf, sampleIDs=None, sample_abd=True):
"""
Calculate the total number of sequences in each OTU or SampleID.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: List
:param sampleIDs: A list of column id's from BIOM format OTU table. By default, the
list has been set to None.
:type sample_abd: Boolean
:param sample_abd: A boolean operator to provide output for OTUID's or SampleID's. By
default, the output will be provided for SampleID's.
:rtype: dict
:return: Returns a dictionary keyed on either OTUID's or SampleIDs and their
respective abundance as values.
"""
results = defaultdict(int)
if sampleIDs is None:
sampleIDs = biomf.ids()
else:
try:
for sid in sampleIDs:
assert sid in biomf.ids()
except AssertionError:
raise ValueError(
"\nError while calculating raw total abundances: The sampleIDs provided "
"do not match the sampleIDs in biom file. Please double check the "
"sampleIDs provided.\n")
otuIDs = biomf.ids(axis="observation")
for sampleID in sampleIDs:
for otuID in otuIDs:
abd = biomf.get_value_by_ids(otuID, sampleID)
if sample_abd:
results[sampleID] += abd
else:
results[otuID] += abd
return results
|
python
|
def raw_abundance(biomf, sampleIDs=None, sample_abd=True):
"""
Calculate the total number of sequences in each OTU or SampleID.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: List
:param sampleIDs: A list of column id's from BIOM format OTU table. By default, the
list has been set to None.
:type sample_abd: Boolean
:param sample_abd: A boolean operator to provide output for OTUID's or SampleID's. By
default, the output will be provided for SampleID's.
:rtype: dict
:return: Returns a dictionary keyed on either OTUID's or SampleIDs and their
respective abundance as values.
"""
results = defaultdict(int)
if sampleIDs is None:
sampleIDs = biomf.ids()
else:
try:
for sid in sampleIDs:
assert sid in biomf.ids()
except AssertionError:
raise ValueError(
"\nError while calculating raw total abundances: The sampleIDs provided "
"do not match the sampleIDs in biom file. Please double check the "
"sampleIDs provided.\n")
otuIDs = biomf.ids(axis="observation")
for sampleID in sampleIDs:
for otuID in otuIDs:
abd = biomf.get_value_by_ids(otuID, sampleID)
if sample_abd:
results[sampleID] += abd
else:
results[otuID] += abd
return results
|
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"[",
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] |
Calculate the total number of sequences in each OTU or SampleID.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:type sampleIDs: List
:param sampleIDs: A list of column id's from BIOM format OTU table. By default, the
list has been set to None.
:type sample_abd: Boolean
:param sample_abd: A boolean operator to provide output for OTUID's or SampleID's. By
default, the output will be provided for SampleID's.
:rtype: dict
:return: Returns a dictionary keyed on either OTUID's or SampleIDs and their
respective abundance as values.
|
[
"Calculate",
"the",
"total",
"number",
"of",
"sequences",
"in",
"each",
"OTU",
"or",
"SampleID",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L95-L135
|
train
|
smdabdoub/phylotoast
|
phylotoast/biom_calc.py
|
transform_raw_abundance
|
def transform_raw_abundance(biomf, fn=math.log10, sampleIDs=None, sample_abd=True):
"""
Function to transform the total abundance calculation for each sample ID to another
format based on user given transformation function.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:param fn: Mathematical function which is used to transform smax to another format.
By default, the function has been given as base 10 logarithm.
:rtype: dict
:return: Returns a dictionary similar to output of raw_abundance function but with
the abundance values modified by the mathematical operation. By default, the
operation performed on the abundances is base 10 logarithm.
"""
totals = raw_abundance(biomf, sampleIDs, sample_abd)
return {sid: fn(abd) for sid, abd in totals.items()}
|
python
|
def transform_raw_abundance(biomf, fn=math.log10, sampleIDs=None, sample_abd=True):
"""
Function to transform the total abundance calculation for each sample ID to another
format based on user given transformation function.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:param fn: Mathematical function which is used to transform smax to another format.
By default, the function has been given as base 10 logarithm.
:rtype: dict
:return: Returns a dictionary similar to output of raw_abundance function but with
the abundance values modified by the mathematical operation. By default, the
operation performed on the abundances is base 10 logarithm.
"""
totals = raw_abundance(biomf, sampleIDs, sample_abd)
return {sid: fn(abd) for sid, abd in totals.items()}
|
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"(",
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] |
Function to transform the total abundance calculation for each sample ID to another
format based on user given transformation function.
:type biomf: A BIOM file.
:param biomf: OTU table format.
:param fn: Mathematical function which is used to transform smax to another format.
By default, the function has been given as base 10 logarithm.
:rtype: dict
:return: Returns a dictionary similar to output of raw_abundance function but with
the abundance values modified by the mathematical operation. By default, the
operation performed on the abundances is base 10 logarithm.
|
[
"Function",
"to",
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"the",
"total",
"abundance",
"calculation",
"for",
"each",
"sample",
"ID",
"to",
"another",
"format",
"based",
"on",
"user",
"given",
"transformation",
"function",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L138-L155
|
train
|
smdabdoub/phylotoast
|
bin/diversity.py
|
print_MannWhitneyU
|
def print_MannWhitneyU(div_calc):
"""
Compute the Mann-Whitney U test for unequal group sample sizes.
"""
try:
x = div_calc.values()[0].values()
y = div_calc.values()[1].values()
except:
return "Error setting up input arrays for Mann-Whitney U Test. Skipping "\
"significance testing."
T, p = stats.mannwhitneyu(x, y)
print "\nMann-Whitney U test statistic:", T
print "Two-tailed p-value: {}".format(2 * p)
|
python
|
def print_MannWhitneyU(div_calc):
"""
Compute the Mann-Whitney U test for unequal group sample sizes.
"""
try:
x = div_calc.values()[0].values()
y = div_calc.values()[1].values()
except:
return "Error setting up input arrays for Mann-Whitney U Test. Skipping "\
"significance testing."
T, p = stats.mannwhitneyu(x, y)
print "\nMann-Whitney U test statistic:", T
print "Two-tailed p-value: {}".format(2 * p)
|
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Compute the Mann-Whitney U test for unequal group sample sizes.
|
[
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"for",
"unequal",
"group",
"sample",
"sizes",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L54-L66
|
train
|
smdabdoub/phylotoast
|
bin/diversity.py
|
print_KruskalWallisH
|
def print_KruskalWallisH(div_calc):
"""
Compute the Kruskal-Wallis H-test for independent samples. A typical rule is that
each group must have at least 5 measurements.
"""
calc = defaultdict(list)
try:
for k1, v1 in div_calc.iteritems():
for k2, v2 in v1.iteritems():
calc[k1].append(v2)
except:
return "Error setting up input arrays for Kruskal-Wallis H-Test. Skipping "\
"significance testing."
h, p = stats.kruskal(*calc.values())
print "\nKruskal-Wallis H-test statistic for {} groups: {}".format(str(len(div_calc)), h)
print "p-value: {}".format(p)
|
python
|
def print_KruskalWallisH(div_calc):
"""
Compute the Kruskal-Wallis H-test for independent samples. A typical rule is that
each group must have at least 5 measurements.
"""
calc = defaultdict(list)
try:
for k1, v1 in div_calc.iteritems():
for k2, v2 in v1.iteritems():
calc[k1].append(v2)
except:
return "Error setting up input arrays for Kruskal-Wallis H-Test. Skipping "\
"significance testing."
h, p = stats.kruskal(*calc.values())
print "\nKruskal-Wallis H-test statistic for {} groups: {}".format(str(len(div_calc)), h)
print "p-value: {}".format(p)
|
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Compute the Kruskal-Wallis H-test for independent samples. A typical rule is that
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|
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L69-L84
|
train
|
smdabdoub/phylotoast
|
bin/diversity.py
|
handle_program_options
|
def handle_program_options():
"""Parses the given options passed in at the command line."""
parser = argparse.ArgumentParser(description="Calculate the alpha diversity\
of a set of samples using one or more \
metrics and output a kernal density \
estimator-smoothed histogram of the \
results.")
parser.add_argument("-m", "--map_file",
help="QIIME mapping file.")
parser.add_argument("-i", "--biom_fp",
help="Path to the BIOM table")
parser.add_argument("-c", "--category",
help="Specific category from the mapping file.")
parser.add_argument("-d", "--diversity", default=["shannon"], nargs="+",
help="The alpha diversity metric. Default \
value is 'shannon', which will calculate the Shannon\
entropy. Multiple metrics can be specified (space separated).\
The full list of metrics is available at:\
http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.\
Beta diversity metrics will be supported in the future.")
parser.add_argument("--x_label", default=[None], nargs="+",
help="The name of the diversity metric to be displayed on the\
plot as the X-axis label. If multiple metrics are specified,\
then multiple entries for the X-axis label should be given.")
parser.add_argument("--color_by",
help="A column name in the mapping file containing\
hexadecimal (#FF0000) color values that will\
be used to color the groups. Each sample ID must\
have a color entry.")
parser.add_argument("--plot_title", default="",
help="A descriptive title that will appear at the top \
of the output plot. Surround with quotes if there are\
spaces in the title.")
parser.add_argument("-o", "--output_dir", default=".",
help="The directory plots will be saved to.")
parser.add_argument("--image_type", default="png",
help="The type of image to save: png, svg, pdf, eps, etc...")
parser.add_argument("--save_calculations",
help="Path and name of text file to store the calculated "
"diversity metrics.")
parser.add_argument("--suppress_stats", action="store_true", help="Do not display "
"significance testing results which are shown by default.")
parser.add_argument("--show_available_metrics", action="store_true",
help="Supply this parameter to see which alpha diversity metrics "
" are available for usage. No calculations will be performed"
" if this parameter is provided.")
return parser.parse_args()
|
python
|
def handle_program_options():
"""Parses the given options passed in at the command line."""
parser = argparse.ArgumentParser(description="Calculate the alpha diversity\
of a set of samples using one or more \
metrics and output a kernal density \
estimator-smoothed histogram of the \
results.")
parser.add_argument("-m", "--map_file",
help="QIIME mapping file.")
parser.add_argument("-i", "--biom_fp",
help="Path to the BIOM table")
parser.add_argument("-c", "--category",
help="Specific category from the mapping file.")
parser.add_argument("-d", "--diversity", default=["shannon"], nargs="+",
help="The alpha diversity metric. Default \
value is 'shannon', which will calculate the Shannon\
entropy. Multiple metrics can be specified (space separated).\
The full list of metrics is available at:\
http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.\
Beta diversity metrics will be supported in the future.")
parser.add_argument("--x_label", default=[None], nargs="+",
help="The name of the diversity metric to be displayed on the\
plot as the X-axis label. If multiple metrics are specified,\
then multiple entries for the X-axis label should be given.")
parser.add_argument("--color_by",
help="A column name in the mapping file containing\
hexadecimal (#FF0000) color values that will\
be used to color the groups. Each sample ID must\
have a color entry.")
parser.add_argument("--plot_title", default="",
help="A descriptive title that will appear at the top \
of the output plot. Surround with quotes if there are\
spaces in the title.")
parser.add_argument("-o", "--output_dir", default=".",
help="The directory plots will be saved to.")
parser.add_argument("--image_type", default="png",
help="The type of image to save: png, svg, pdf, eps, etc...")
parser.add_argument("--save_calculations",
help="Path and name of text file to store the calculated "
"diversity metrics.")
parser.add_argument("--suppress_stats", action="store_true", help="Do not display "
"significance testing results which are shown by default.")
parser.add_argument("--show_available_metrics", action="store_true",
help="Supply this parameter to see which alpha diversity metrics "
" are available for usage. No calculations will be performed"
" if this parameter is provided.")
return parser.parse_args()
|
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"(",
"\"--color_by\"",
",",
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"\"A column name in the mapping file containing\\\n hexadecimal (#FF0000) color values that will\\\n be used to color the groups. Each sample ID must\\\n have a color entry.\"",
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"(",
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",",
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",",
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"help",
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"(",
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"action",
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",",
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"\" are available for usage. No calculations will be performed\"",
"\" if this parameter is provided.\"",
")",
"return",
"parser",
".",
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"(",
")"
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Parses the given options passed in at the command line.
|
[
"Parses",
"the",
"given",
"options",
"passed",
"in",
"at",
"the",
"command",
"line",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L122-L168
|
train
|
christophertbrown/bioscripts
|
ctbBio/search.py
|
blastdb
|
def blastdb(fasta, maxfile = 10000000):
"""
make blast db
"""
db = fasta.rsplit('.', 1)[0]
type = check_type(fasta)
if type == 'nucl':
type = ['nhr', type]
else:
type = ['phr', type]
if os.path.exists('%s.%s' % (db, type[0])) is False \
and os.path.exists('%s.00.%s' % (db, type[0])) is False:
print('# ... making blastdb for: %s' % (fasta), file=sys.stderr)
os.system('makeblastdb \
-in %s -out %s -dbtype %s -max_file_sz %s >> log.txt' \
% (fasta, db, type[1], maxfile))
else:
print('# ... database found for: %s' % (fasta), file=sys.stderr)
return db
|
python
|
def blastdb(fasta, maxfile = 10000000):
"""
make blast db
"""
db = fasta.rsplit('.', 1)[0]
type = check_type(fasta)
if type == 'nucl':
type = ['nhr', type]
else:
type = ['phr', type]
if os.path.exists('%s.%s' % (db, type[0])) is False \
and os.path.exists('%s.00.%s' % (db, type[0])) is False:
print('# ... making blastdb for: %s' % (fasta), file=sys.stderr)
os.system('makeblastdb \
-in %s -out %s -dbtype %s -max_file_sz %s >> log.txt' \
% (fasta, db, type[1], maxfile))
else:
print('# ... database found for: %s' % (fasta), file=sys.stderr)
return db
|
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make blast db
|
[
"make",
"blast",
"db"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/search.py#L28-L46
|
train
|
christophertbrown/bioscripts
|
ctbBio/search.py
|
usearchdb
|
def usearchdb(fasta, alignment = 'local', usearch_loc = 'usearch'):
"""
make usearch db
"""
if '.udb' in fasta:
print('# ... database found: %s' % (fasta), file=sys.stderr)
return fasta
type = check_type(fasta)
db = '%s.%s.udb' % (fasta.rsplit('.', 1)[0], type)
if os.path.exists(db) is False:
print('# ... making usearch db for: %s' % (fasta), file=sys.stderr)
if alignment == 'local':
os.system('%s -makeudb_ublast %s -output %s >> log.txt' % (usearch_loc, fasta, db))
elif alignment == 'global':
os.system('%s -makeudb_usearch %s -output %s >> log.txt' % (usearch_loc, fasta, db))
else:
print('# ... database found for: %s' % (fasta), file=sys.stderr)
return db
|
python
|
def usearchdb(fasta, alignment = 'local', usearch_loc = 'usearch'):
"""
make usearch db
"""
if '.udb' in fasta:
print('# ... database found: %s' % (fasta), file=sys.stderr)
return fasta
type = check_type(fasta)
db = '%s.%s.udb' % (fasta.rsplit('.', 1)[0], type)
if os.path.exists(db) is False:
print('# ... making usearch db for: %s' % (fasta), file=sys.stderr)
if alignment == 'local':
os.system('%s -makeudb_ublast %s -output %s >> log.txt' % (usearch_loc, fasta, db))
elif alignment == 'global':
os.system('%s -makeudb_usearch %s -output %s >> log.txt' % (usearch_loc, fasta, db))
else:
print('# ... database found for: %s' % (fasta), file=sys.stderr)
return db
|
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] |
make usearch db
|
[
"make",
"usearch",
"db"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/search.py#L68-L85
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/control.py
|
_pp
|
def _pp(dict_data):
"""Pretty print."""
for key, val in dict_data.items():
# pylint: disable=superfluous-parens
print('{0:<11}: {1}'.format(key, val))
|
python
|
def _pp(dict_data):
"""Pretty print."""
for key, val in dict_data.items():
# pylint: disable=superfluous-parens
print('{0:<11}: {1}'.format(key, val))
|
[
"def",
"_pp",
"(",
"dict_data",
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":",
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"key",
",",
"val",
"in",
"dict_data",
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")",
":",
"# pylint: disable=superfluous-parens",
"print",
"(",
"'{0:<11}: {1}'",
".",
"format",
"(",
"key",
",",
"val",
")",
")"
] |
Pretty print.
|
[
"Pretty",
"print",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L11-L15
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/control.py
|
print_licences
|
def print_licences(params, metadata):
"""Print licenses.
:param argparse.Namespace params: parameter
:param bootstrap_py.classifier.Classifiers metadata: package metadata
"""
if hasattr(params, 'licenses'):
if params.licenses:
_pp(metadata.licenses_desc())
sys.exit(0)
|
python
|
def print_licences(params, metadata):
"""Print licenses.
:param argparse.Namespace params: parameter
:param bootstrap_py.classifier.Classifiers metadata: package metadata
"""
if hasattr(params, 'licenses'):
if params.licenses:
_pp(metadata.licenses_desc())
sys.exit(0)
|
[
"def",
"print_licences",
"(",
"params",
",",
"metadata",
")",
":",
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"hasattr",
"(",
"params",
",",
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"(",
"metadata",
".",
"licenses_desc",
"(",
")",
")",
"sys",
".",
"exit",
"(",
"0",
")"
] |
Print licenses.
:param argparse.Namespace params: parameter
:param bootstrap_py.classifier.Classifiers metadata: package metadata
|
[
"Print",
"licenses",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L27-L36
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/control.py
|
check_repository_existence
|
def check_repository_existence(params):
"""Check repository existence.
:param argparse.Namespace params: parameters
"""
repodir = os.path.join(params.outdir, params.name)
if os.path.isdir(repodir):
raise Conflict(
'Package repository "{0}" has already exists.'.format(repodir))
|
python
|
def check_repository_existence(params):
"""Check repository existence.
:param argparse.Namespace params: parameters
"""
repodir = os.path.join(params.outdir, params.name)
if os.path.isdir(repodir):
raise Conflict(
'Package repository "{0}" has already exists.'.format(repodir))
|
[
"def",
"check_repository_existence",
"(",
"params",
")",
":",
"repodir",
"=",
"os",
".",
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".",
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"(",
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".",
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",",
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"repodir",
")",
":",
"raise",
"Conflict",
"(",
"'Package repository \"{0}\" has already exists.'",
".",
"format",
"(",
"repodir",
")",
")"
] |
Check repository existence.
:param argparse.Namespace params: parameters
|
[
"Check",
"repository",
"existence",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L39-L47
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/control.py
|
generate_package
|
def generate_package(params):
"""Generate package repository.
:param argparse.Namespace params: parameters
"""
pkg_data = package.PackageData(params)
pkg_tree = package.PackageTree(pkg_data)
pkg_tree.generate()
pkg_tree.move()
VCS(os.path.join(pkg_tree.outdir, pkg_tree.name), pkg_tree.pkg_data)
|
python
|
def generate_package(params):
"""Generate package repository.
:param argparse.Namespace params: parameters
"""
pkg_data = package.PackageData(params)
pkg_tree = package.PackageTree(pkg_data)
pkg_tree.generate()
pkg_tree.move()
VCS(os.path.join(pkg_tree.outdir, pkg_tree.name), pkg_tree.pkg_data)
|
[
"def",
"generate_package",
"(",
"params",
")",
":",
"pkg_data",
"=",
"package",
".",
"PackageData",
"(",
"params",
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"PackageTree",
"(",
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",",
"pkg_tree",
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")",
",",
"pkg_tree",
".",
"pkg_data",
")"
] |
Generate package repository.
:param argparse.Namespace params: parameters
|
[
"Generate",
"package",
"repository",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L59-L68
|
train
|
christophertbrown/bioscripts
|
ctbBio/sam2fastq.py
|
print_single
|
def print_single(line, rev):
"""
print single reads to stderr
"""
if rev is True:
seq = rc(['', line[9]])[1]
qual = line[10][::-1]
else:
seq = line[9]
qual = line[10]
fq = ['@%s' % line[0], seq, '+%s' % line[0], qual]
print('\n'.join(fq), file = sys.stderr)
|
python
|
def print_single(line, rev):
"""
print single reads to stderr
"""
if rev is True:
seq = rc(['', line[9]])[1]
qual = line[10][::-1]
else:
seq = line[9]
qual = line[10]
fq = ['@%s' % line[0], seq, '+%s' % line[0], qual]
print('\n'.join(fq), file = sys.stderr)
|
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"(",
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"=",
"sys",
".",
"stderr",
")"
] |
print single reads to stderr
|
[
"print",
"single",
"reads",
"to",
"stderr"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/sam2fastq.py#L13-L24
|
train
|
christophertbrown/bioscripts
|
ctbBio/sam2fastq.py
|
sam2fastq
|
def sam2fastq(sam, singles = False, force = False):
"""
convert sam to fastq
"""
L, R = None, None
for line in sam:
if line.startswith('@') is True:
continue
line = line.strip().split()
bit = [True if i == '1' else False \
for i in bin(int(line[1])).split('b')[1][::-1]]
while len(bit) < 8:
bit.append(False)
pair, proper, na, nap, rev, mrev, left, right = bit
# make sure read is paired
if pair is False:
if singles is True:
print_single(line, rev)
continue
# check if sequence is reverse-complemented
if rev is True:
seq = rc(['', line[9]])[1]
qual = line[10][::-1]
else:
seq = line[9]
qual = line[10]
# check if read is forward or reverse, return when both have been found
if left is True:
if L is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if L is not None:
L = None
continue
L = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if R is not None:
yield L
yield R
L, R = None, None
if right is True:
if R is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if R is not None:
R = None
continue
R = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if L is not None:
yield L
yield R
L, R = None, None
|
python
|
def sam2fastq(sam, singles = False, force = False):
"""
convert sam to fastq
"""
L, R = None, None
for line in sam:
if line.startswith('@') is True:
continue
line = line.strip().split()
bit = [True if i == '1' else False \
for i in bin(int(line[1])).split('b')[1][::-1]]
while len(bit) < 8:
bit.append(False)
pair, proper, na, nap, rev, mrev, left, right = bit
# make sure read is paired
if pair is False:
if singles is True:
print_single(line, rev)
continue
# check if sequence is reverse-complemented
if rev is True:
seq = rc(['', line[9]])[1]
qual = line[10][::-1]
else:
seq = line[9]
qual = line[10]
# check if read is forward or reverse, return when both have been found
if left is True:
if L is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if L is not None:
L = None
continue
L = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if R is not None:
yield L
yield R
L, R = None, None
if right is True:
if R is not None and force is False:
print('sam file is not sorted', file = sys.stderr)
print('\te.g.: %s' % (line[0]), file = sys.stderr)
exit()
if R is not None:
R = None
continue
R = ['@%s' % line[0], seq, '+%s' % line[0], qual]
if L is not None:
yield L
yield R
L, R = None, None
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convert sam to fastq
|
[
"convert",
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83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/sam2fastq.py#L26-L78
|
train
|
christophertbrown/bioscripts
|
ctbBio/subset_sam.py
|
sort_sam
|
def sort_sam(sam, sort):
"""
sort sam file
"""
tempdir = '%s/' % (os.path.abspath(sam).rsplit('/', 1)[0])
if sort is True:
mapping = '%s.sorted.sam' % (sam.rsplit('.', 1)[0])
if sam != '-':
if os.path.exists(mapping) is False:
os.system("\
sort -k1 --buffer-size=%sG -T %s -o %s %s\
" % (sbuffer, tempdir, mapping, sam))
else:
mapping = 'stdin-sam.sorted.sam'
p = Popen("sort -k1 --buffer-size=%sG -T %s -o %s" \
% (sbuffer, tempdir, mapping), stdin = sys.stdin, shell = True)
p.communicate()
mapping = open(mapping)
else:
if sam == '-':
mapping = sys.stdin
else:
mapping = open(sam)
return mapping
|
python
|
def sort_sam(sam, sort):
"""
sort sam file
"""
tempdir = '%s/' % (os.path.abspath(sam).rsplit('/', 1)[0])
if sort is True:
mapping = '%s.sorted.sam' % (sam.rsplit('.', 1)[0])
if sam != '-':
if os.path.exists(mapping) is False:
os.system("\
sort -k1 --buffer-size=%sG -T %s -o %s %s\
" % (sbuffer, tempdir, mapping, sam))
else:
mapping = 'stdin-sam.sorted.sam'
p = Popen("sort -k1 --buffer-size=%sG -T %s -o %s" \
% (sbuffer, tempdir, mapping), stdin = sys.stdin, shell = True)
p.communicate()
mapping = open(mapping)
else:
if sam == '-':
mapping = sys.stdin
else:
mapping = open(sam)
return mapping
|
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sort sam file
|
[
"sort",
"sam",
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83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/subset_sam.py#L14-L37
|
train
|
christophertbrown/bioscripts
|
ctbBio/subset_sam.py
|
sub_sam
|
def sub_sam(sam, percent, sort = True, sbuffer = False):
"""
randomly subset sam file
"""
mapping = sort_sam(sam, sort)
pool = [1 for i in range(0, percent)] + [0 for i in range(0, 100 - percent)]
c = cycle([1, 2])
for line in mapping:
line = line.strip().split()
if line[0].startswith('@'): # get the sam header
yield line
continue
if int(line[1]) <= 20: # is this from a single read?
if random.choice(pool) == 1:
yield line
else:
n = next(c)
if n == 1:
prev = line
if n == 2 and random.choice(pool) == 1:
yield prev
yield line
|
python
|
def sub_sam(sam, percent, sort = True, sbuffer = False):
"""
randomly subset sam file
"""
mapping = sort_sam(sam, sort)
pool = [1 for i in range(0, percent)] + [0 for i in range(0, 100 - percent)]
c = cycle([1, 2])
for line in mapping:
line = line.strip().split()
if line[0].startswith('@'): # get the sam header
yield line
continue
if int(line[1]) <= 20: # is this from a single read?
if random.choice(pool) == 1:
yield line
else:
n = next(c)
if n == 1:
prev = line
if n == 2 and random.choice(pool) == 1:
yield prev
yield line
|
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randomly subset sam file
|
[
"randomly",
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] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/subset_sam.py#L39-L60
|
train
|
christophertbrown/bioscripts
|
ctbBio/fastq2fasta.py
|
fq2fa
|
def fq2fa(fq):
"""
convert fq to fa
"""
c = cycle([1, 2, 3, 4])
for line in fq:
n = next(c)
if n == 1:
seq = ['>%s' % (line.strip().split('@', 1)[1])]
if n == 2:
seq.append(line.strip())
yield seq
|
python
|
def fq2fa(fq):
"""
convert fq to fa
"""
c = cycle([1, 2, 3, 4])
for line in fq:
n = next(c)
if n == 1:
seq = ['>%s' % (line.strip().split('@', 1)[1])]
if n == 2:
seq.append(line.strip())
yield seq
|
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convert fq to fa
|
[
"convert",
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83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/fastq2fasta.py#L11-L22
|
train
|
elbow-jason/Uno-deprecated
|
uno/decorators.py
|
change_return_type
|
def change_return_type(f):
"""
Converts the returned value of wrapped function to the type of the
first arg or to the type specified by a kwarg key return_type's value.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
return return_type(f(*args, **kwargs))
elif len(args) > 0:
return_type = type(args[0])
return return_type(f(*args, **kwargs))
else:
return f(*args, **kwargs)
return wrapper
|
python
|
def change_return_type(f):
"""
Converts the returned value of wrapped function to the type of the
first arg or to the type specified by a kwarg key return_type's value.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
return return_type(f(*args, **kwargs))
elif len(args) > 0:
return_type = type(args[0])
return return_type(f(*args, **kwargs))
else:
return f(*args, **kwargs)
return wrapper
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4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4
|
https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/decorators.py#L11-L27
|
train
|
elbow-jason/Uno-deprecated
|
uno/decorators.py
|
convert_args_to_sets
|
def convert_args_to_sets(f):
"""
Converts all args to 'set' type via self.setify function.
"""
@wraps(f)
def wrapper(*args, **kwargs):
args = (setify(x) for x in args)
return f(*args, **kwargs)
return wrapper
|
python
|
def convert_args_to_sets(f):
"""
Converts all args to 'set' type via self.setify function.
"""
@wraps(f)
def wrapper(*args, **kwargs):
args = (setify(x) for x in args)
return f(*args, **kwargs)
return wrapper
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4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4
|
https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/decorators.py#L30-L38
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
KBBI._init_entri
|
def _init_entri(self, laman):
"""Membuat objek-objek entri dari laman yang diambil.
:param laman: Laman respons yang dikembalikan oleh KBBI daring.
:type laman: Response
"""
sup = BeautifulSoup(laman.text, 'html.parser')
estr = ''
for label in sup.find('hr').next_siblings:
if label.name == 'hr':
self.entri.append(Entri(estr))
break
if label.name == 'h2':
if estr:
self.entri.append(Entri(estr))
estr = ''
estr += str(label).strip()
|
python
|
def _init_entri(self, laman):
"""Membuat objek-objek entri dari laman yang diambil.
:param laman: Laman respons yang dikembalikan oleh KBBI daring.
:type laman: Response
"""
sup = BeautifulSoup(laman.text, 'html.parser')
estr = ''
for label in sup.find('hr').next_siblings:
if label.name == 'hr':
self.entri.append(Entri(estr))
break
if label.name == 'h2':
if estr:
self.entri.append(Entri(estr))
estr = ''
estr += str(label).strip()
|
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"''",
"estr",
"+=",
"str",
"(",
"label",
")",
".",
"strip",
"(",
")"
] |
Membuat objek-objek entri dari laman yang diambil.
:param laman: Laman respons yang dikembalikan oleh KBBI daring.
:type laman: Response
|
[
"Membuat",
"objek",
"-",
"objek",
"entri",
"dari",
"laman",
"yang",
"diambil",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L46-L63
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Entri._init_kata_dasar
|
def _init_kata_dasar(self, dasar):
"""Memproses kata dasar yang ada dalam nama entri.
:param dasar: ResultSet untuk label HTML dengan class="rootword"
:type dasar: ResultSet
"""
for tiap in dasar:
kata = tiap.find('a')
dasar_no = kata.find('sup')
kata = ambil_teks_dalam_label(kata)
self.kata_dasar.append(
kata + ' [{}]'.format(dasar_no.text.strip()) if dasar_no else kata
)
|
python
|
def _init_kata_dasar(self, dasar):
"""Memproses kata dasar yang ada dalam nama entri.
:param dasar: ResultSet untuk label HTML dengan class="rootword"
:type dasar: ResultSet
"""
for tiap in dasar:
kata = tiap.find('a')
dasar_no = kata.find('sup')
kata = ambil_teks_dalam_label(kata)
self.kata_dasar.append(
kata + ' [{}]'.format(dasar_no.text.strip()) if dasar_no else kata
)
|
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"text",
".",
"strip",
"(",
")",
")",
"if",
"dasar_no",
"else",
"kata",
")"
] |
Memproses kata dasar yang ada dalam nama entri.
:param dasar: ResultSet untuk label HTML dengan class="rootword"
:type dasar: ResultSet
|
[
"Memproses",
"kata",
"dasar",
"yang",
"ada",
"dalam",
"nama",
"entri",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L126-L139
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Entri.serialisasi
|
def serialisasi(self):
"""Mengembalikan hasil serialisasi objek Entri ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
"""
return {
"nama": self.nama,
"nomor": self.nomor,
"kata_dasar": self.kata_dasar,
"pelafalan": self.pelafalan,
"bentuk_tidak_baku": self.bentuk_tidak_baku,
"varian": self.varian,
"makna": [makna.serialisasi() for makna in self.makna]
}
|
python
|
def serialisasi(self):
"""Mengembalikan hasil serialisasi objek Entri ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
"""
return {
"nama": self.nama,
"nomor": self.nomor,
"kata_dasar": self.kata_dasar,
"pelafalan": self.pelafalan,
"bentuk_tidak_baku": self.bentuk_tidak_baku,
"varian": self.varian,
"makna": [makna.serialisasi() for makna in self.makna]
}
|
[
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":",
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"\"nomor\"",
":",
"self",
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"nomor",
",",
"\"kata_dasar\"",
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",",
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"\"bentuk_tidak_baku\"",
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"(",
")",
"for",
"makna",
"in",
"self",
".",
"makna",
"]",
"}"
] |
Mengembalikan hasil serialisasi objek Entri ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
|
[
"Mengembalikan",
"hasil",
"serialisasi",
"objek",
"Entri",
"ini",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L141-L156
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Entri._makna
|
def _makna(self):
"""Mengembalikan representasi string untuk semua makna entri ini.
:returns: String representasi makna-makna
:rtype: str
"""
if len(self.makna) > 1:
return '\n'.join(
str(i) + ". " + str(makna)
for i, makna in enumerate(self.makna, 1)
)
return str(self.makna[0])
|
python
|
def _makna(self):
"""Mengembalikan representasi string untuk semua makna entri ini.
:returns: String representasi makna-makna
:rtype: str
"""
if len(self.makna) > 1:
return '\n'.join(
str(i) + ". " + str(makna)
for i, makna in enumerate(self.makna, 1)
)
return str(self.makna[0])
|
[
"def",
"_makna",
"(",
"self",
")",
":",
"if",
"len",
"(",
"self",
".",
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")",
">",
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"'\\n'",
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"join",
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"1",
")",
")",
"return",
"str",
"(",
"self",
".",
"makna",
"[",
"0",
"]",
")"
] |
Mengembalikan representasi string untuk semua makna entri ini.
:returns: String representasi makna-makna
:rtype: str
|
[
"Mengembalikan",
"representasi",
"string",
"untuk",
"semua",
"makna",
"entri",
"ini",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L158-L170
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Entri._nama
|
def _nama(self):
"""Mengembalikan representasi string untuk nama entri ini.
:returns: String representasi nama entri
:rtype: str
"""
hasil = self.nama
if self.nomor:
hasil += " [{}]".format(self.nomor)
if self.kata_dasar:
hasil = " » ".join(self.kata_dasar) + " » " + hasil
return hasil
|
python
|
def _nama(self):
"""Mengembalikan representasi string untuk nama entri ini.
:returns: String representasi nama entri
:rtype: str
"""
hasil = self.nama
if self.nomor:
hasil += " [{}]".format(self.nomor)
if self.kata_dasar:
hasil = " » ".join(self.kata_dasar) + " » " + hasil
return hasil
|
[
"def",
"_nama",
"(",
"self",
")",
":",
"hasil",
"=",
"self",
".",
"nama",
"if",
"self",
".",
"nomor",
":",
"hasil",
"+=",
"\" [{}]\"",
".",
"format",
"(",
"self",
".",
"nomor",
")",
"if",
"self",
".",
"kata_dasar",
":",
"hasil",
"=",
"\" » \".",
"j",
"oin(",
"s",
"elf.",
"k",
"ata_dasar)",
" ",
" ",
" » \" +",
"h",
"sil",
"return",
"hasil"
] |
Mengembalikan representasi string untuk nama entri ini.
:returns: String representasi nama entri
:rtype: str
|
[
"Mengembalikan",
"representasi",
"string",
"untuk",
"nama",
"entri",
"ini",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L172-L184
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Entri._varian
|
def _varian(self, varian):
"""Mengembalikan representasi string untuk varian entri ini.
Dapat digunakan untuk "Varian" maupun "Bentuk tidak baku".
:param varian: List bentuk tidak baku atau varian
:type varian: list
:returns: String representasi varian atau bentuk tidak baku
:rtype: str
"""
if varian == self.bentuk_tidak_baku:
nama = "Bentuk tidak baku"
elif varian == self.varian:
nama = "Varian"
else:
return ''
return nama + ': ' + ', '.join(varian)
|
python
|
def _varian(self, varian):
"""Mengembalikan representasi string untuk varian entri ini.
Dapat digunakan untuk "Varian" maupun "Bentuk tidak baku".
:param varian: List bentuk tidak baku atau varian
:type varian: list
:returns: String representasi varian atau bentuk tidak baku
:rtype: str
"""
if varian == self.bentuk_tidak_baku:
nama = "Bentuk tidak baku"
elif varian == self.varian:
nama = "Varian"
else:
return ''
return nama + ': ' + ', '.join(varian)
|
[
"def",
"_varian",
"(",
"self",
",",
"varian",
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":",
"if",
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"==",
"self",
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":",
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"\"Bentuk tidak baku\"",
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"==",
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"varian",
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"\"Varian\"",
"else",
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"''",
"return",
"nama",
"+",
"': '",
"+",
"', '",
".",
"join",
"(",
"varian",
")"
] |
Mengembalikan representasi string untuk varian entri ini.
Dapat digunakan untuk "Varian" maupun "Bentuk tidak baku".
:param varian: List bentuk tidak baku atau varian
:type varian: list
:returns: String representasi varian atau bentuk tidak baku
:rtype: str
|
[
"Mengembalikan",
"representasi",
"string",
"untuk",
"varian",
"entri",
"ini",
".",
"Dapat",
"digunakan",
"untuk",
"Varian",
"maupun",
"Bentuk",
"tidak",
"baku",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L186-L202
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Makna._init_kelas
|
def _init_kelas(self, makna_label):
"""Memproses kelas kata yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
"""
kelas = makna_label.find(color='red')
lain = makna_label.find(color='darkgreen')
info = makna_label.find(color='green')
if kelas:
kelas = kelas.find_all('span')
if lain:
self.kelas = {lain.text.strip(): lain['title'].strip()}
self.submakna = lain.next_sibling.strip()
self.submakna += ' ' + makna_label.find(color='grey').text.strip()
else:
self.kelas = {
k.text.strip(): k['title'].strip() for k in kelas
} if kelas else {}
self.info = info.text.strip() if info else ''
|
python
|
def _init_kelas(self, makna_label):
"""Memproses kelas kata yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
"""
kelas = makna_label.find(color='red')
lain = makna_label.find(color='darkgreen')
info = makna_label.find(color='green')
if kelas:
kelas = kelas.find_all('span')
if lain:
self.kelas = {lain.text.strip(): lain['title'].strip()}
self.submakna = lain.next_sibling.strip()
self.submakna += ' ' + makna_label.find(color='grey').text.strip()
else:
self.kelas = {
k.text.strip(): k['title'].strip() for k in kelas
} if kelas else {}
self.info = info.text.strip() if info else ''
|
[
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"info",
".",
"text",
".",
"strip",
"(",
")",
"if",
"info",
"else",
"''"
] |
Memproses kelas kata yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
|
[
"Memproses",
"kelas",
"kata",
"yang",
"ada",
"dalam",
"makna",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L239-L259
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Makna._init_contoh
|
def _init_contoh(self, makna_label):
"""Memproses contoh yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
"""
indeks = makna_label.text.find(': ')
if indeks != -1:
contoh = makna_label.text[indeks + 2:].strip()
self.contoh = contoh.split('; ')
else:
self.contoh = []
|
python
|
def _init_contoh(self, makna_label):
"""Memproses contoh yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
"""
indeks = makna_label.text.find(': ')
if indeks != -1:
contoh = makna_label.text[indeks + 2:].strip()
self.contoh = contoh.split('; ')
else:
self.contoh = []
|
[
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"self",
",",
"makna_label",
")",
":",
"indeks",
"=",
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"-",
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"split",
"(",
"'; '",
")",
"else",
":",
"self",
".",
"contoh",
"=",
"[",
"]"
] |
Memproses contoh yang ada dalam makna.
:param makna_label: BeautifulSoup untuk makna yang ingin diproses.
:type makna_label: BeautifulSoup
|
[
"Memproses",
"contoh",
"yang",
"ada",
"dalam",
"makna",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L261-L273
|
train
|
laymonage/kbbi-python
|
kbbi/kbbi.py
|
Makna.serialisasi
|
def serialisasi(self):
"""Mengembalikan hasil serialisasi objek Makna ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
"""
return {
"kelas": self.kelas,
"submakna": self.submakna,
"info": self.info,
"contoh": self.contoh
}
|
python
|
def serialisasi(self):
"""Mengembalikan hasil serialisasi objek Makna ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
"""
return {
"kelas": self.kelas,
"submakna": self.submakna,
"info": self.info,
"contoh": self.contoh
}
|
[
"def",
"serialisasi",
"(",
"self",
")",
":",
"return",
"{",
"\"kelas\"",
":",
"self",
".",
"kelas",
",",
"\"submakna\"",
":",
"self",
".",
"submakna",
",",
"\"info\"",
":",
"self",
".",
"info",
",",
"\"contoh\"",
":",
"self",
".",
"contoh",
"}"
] |
Mengembalikan hasil serialisasi objek Makna ini.
:returns: Dictionary hasil serialisasi
:rtype: dict
|
[
"Mengembalikan",
"hasil",
"serialisasi",
"objek",
"Makna",
"ini",
"."
] |
1a52ba8bcc6dc4c5c1215f9e00207aca264287d6
|
https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L275-L287
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/docs.py
|
build_sphinx
|
def build_sphinx(pkg_data, projectdir):
"""Build sphinx documentation.
:rtype: int
:return: subprocess.call return code
:param `bootstrap_py.control.PackageData` pkg_data: package meta data
:param str projectdir: project root directory
"""
try:
version, _minor_version = pkg_data.version.rsplit('.', 1)
except ValueError:
version = pkg_data.version
args = ' '.join(('sphinx-quickstart',
'--sep',
'-q',
'-p "{name}"',
'-a "{author}"',
'-v "{version}"',
'-r "{release}"',
'-l en',
'--suffix=.rst',
'--master=index',
'--ext-autodoc',
'--ext-viewcode',
'--makefile',
'{projectdir}')).format(name=pkg_data.name,
author=pkg_data.author,
version=version,
release=pkg_data.version,
projectdir=projectdir)
if subprocess.call(shlex.split(args)) == 0:
_touch_gitkeep(projectdir)
|
python
|
def build_sphinx(pkg_data, projectdir):
"""Build sphinx documentation.
:rtype: int
:return: subprocess.call return code
:param `bootstrap_py.control.PackageData` pkg_data: package meta data
:param str projectdir: project root directory
"""
try:
version, _minor_version = pkg_data.version.rsplit('.', 1)
except ValueError:
version = pkg_data.version
args = ' '.join(('sphinx-quickstart',
'--sep',
'-q',
'-p "{name}"',
'-a "{author}"',
'-v "{version}"',
'-r "{release}"',
'-l en',
'--suffix=.rst',
'--master=index',
'--ext-autodoc',
'--ext-viewcode',
'--makefile',
'{projectdir}')).format(name=pkg_data.name,
author=pkg_data.author,
version=version,
release=pkg_data.version,
projectdir=projectdir)
if subprocess.call(shlex.split(args)) == 0:
_touch_gitkeep(projectdir)
|
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Build sphinx documentation.
:rtype: int
:return: subprocess.call return code
:param `bootstrap_py.control.PackageData` pkg_data: package meta data
:param str projectdir: project root directory
|
[
"Build",
"sphinx",
"documentation",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/docs.py#L8-L40
|
train
|
christophertbrown/bioscripts
|
ctbBio/crossmap.py
|
bowtiedb
|
def bowtiedb(fa, keepDB):
"""
make bowtie db
"""
btdir = '%s/bt2' % (os.getcwd())
# make directory for
if not os.path.exists(btdir):
os.mkdir(btdir)
btdb = '%s/%s' % (btdir, fa.rsplit('/', 1)[-1])
if keepDB is True:
if os.path.exists('%s.1.bt2' % (btdb)):
return btdb
p = subprocess.Popen('bowtie2-build -q %s %s' \
% (fa, btdb), shell = True)
p.communicate()
return btdb
|
python
|
def bowtiedb(fa, keepDB):
"""
make bowtie db
"""
btdir = '%s/bt2' % (os.getcwd())
# make directory for
if not os.path.exists(btdir):
os.mkdir(btdir)
btdb = '%s/%s' % (btdir, fa.rsplit('/', 1)[-1])
if keepDB is True:
if os.path.exists('%s.1.bt2' % (btdb)):
return btdb
p = subprocess.Popen('bowtie2-build -q %s %s' \
% (fa, btdb), shell = True)
p.communicate()
return btdb
|
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make bowtie db
|
[
"make",
"bowtie",
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] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L16-L31
|
train
|
christophertbrown/bioscripts
|
ctbBio/crossmap.py
|
bowtie
|
def bowtie(sam, btd, f, r, u, opt, no_shrink, threads):
"""
generate bowtie2 command
"""
bt2 = 'bowtie2 -x %s -p %s ' % (btd, threads)
if f is not False:
bt2 += '-1 %s -2 %s ' % (f, r)
if u is not False:
bt2 += '-U %s ' % (u)
bt2 += opt
if no_shrink is False:
if f is False:
bt2 += ' | shrinksam -u -k %s-shrunk.sam ' % (sam)
else:
bt2 += ' | shrinksam -k %s-shrunk.sam ' % (sam)
else:
bt2 += ' > %s.sam' % (sam)
return bt2
|
python
|
def bowtie(sam, btd, f, r, u, opt, no_shrink, threads):
"""
generate bowtie2 command
"""
bt2 = 'bowtie2 -x %s -p %s ' % (btd, threads)
if f is not False:
bt2 += '-1 %s -2 %s ' % (f, r)
if u is not False:
bt2 += '-U %s ' % (u)
bt2 += opt
if no_shrink is False:
if f is False:
bt2 += ' | shrinksam -u -k %s-shrunk.sam ' % (sam)
else:
bt2 += ' | shrinksam -k %s-shrunk.sam ' % (sam)
else:
bt2 += ' > %s.sam' % (sam)
return bt2
|
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generate bowtie2 command
|
[
"generate",
"bowtie2",
"command"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L33-L50
|
train
|
christophertbrown/bioscripts
|
ctbBio/crossmap.py
|
crossmap
|
def crossmap(fas, reads, options, no_shrink, keepDB, threads, cluster, nodes):
"""
map all read sets against all fasta files
"""
if cluster is True:
threads = '48'
btc = []
for fa in fas:
btd = bowtiedb(fa, keepDB)
F, R, U = reads
if F is not False:
if U is False:
u = False
for i, f in enumerate(F):
r = R[i]
if U is not False:
u = U[i]
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], f.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
else:
f = False
r = False
for u in U:
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], u.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
if cluster is False:
for i in btc:
p = subprocess.Popen(i, shell = True)
p.communicate()
else:
ID = ''.join(random.choice([str(i) for i in range(0, 9)]) for _ in range(5))
for node, commands in enumerate(chunks(btc, nodes), 1):
bs = open('%s/crossmap-qsub.%s.%s.sh' % (os.getcwd(), ID, node), 'w')
print('\n'.join(commands), file=bs)
bs.close()
p = subprocess.Popen(\
'qsub -V -N crossmap %s' \
% (bs.name), \
shell = True)
p.communicate()
|
python
|
def crossmap(fas, reads, options, no_shrink, keepDB, threads, cluster, nodes):
"""
map all read sets against all fasta files
"""
if cluster is True:
threads = '48'
btc = []
for fa in fas:
btd = bowtiedb(fa, keepDB)
F, R, U = reads
if F is not False:
if U is False:
u = False
for i, f in enumerate(F):
r = R[i]
if U is not False:
u = U[i]
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], f.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
else:
f = False
r = False
for u in U:
sam = '%s/%s-vs-%s' % (os.getcwd(), \
fa.rsplit('/', 1)[-1], u.rsplit('/', 1)[-1].rsplit('.', 3)[0])
btc.append(bowtie(sam, btd, f, r, u, options, no_shrink, threads))
if cluster is False:
for i in btc:
p = subprocess.Popen(i, shell = True)
p.communicate()
else:
ID = ''.join(random.choice([str(i) for i in range(0, 9)]) for _ in range(5))
for node, commands in enumerate(chunks(btc, nodes), 1):
bs = open('%s/crossmap-qsub.%s.%s.sh' % (os.getcwd(), ID, node), 'w')
print('\n'.join(commands), file=bs)
bs.close()
p = subprocess.Popen(\
'qsub -V -N crossmap %s' \
% (bs.name), \
shell = True)
p.communicate()
|
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map all read sets against all fasta files
|
[
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"against",
"all",
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"files"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L55-L96
|
train
|
disqus/nydus
|
nydus/db/base.py
|
BaseCluster.get_conn
|
def get_conn(self, *args, **kwargs):
"""
Returns a connection object from the router given ``args``.
Useful in cases where a connection cannot be automatically determined
during all steps of the process. An example of this would be
Redis pipelines.
"""
connections = self.__connections_for('get_conn', args=args, kwargs=kwargs)
if len(connections) is 1:
return connections[0]
else:
return connections
|
python
|
def get_conn(self, *args, **kwargs):
"""
Returns a connection object from the router given ``args``.
Useful in cases where a connection cannot be automatically determined
during all steps of the process. An example of this would be
Redis pipelines.
"""
connections = self.__connections_for('get_conn', args=args, kwargs=kwargs)
if len(connections) is 1:
return connections[0]
else:
return connections
|
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Returns a connection object from the router given ``args``.
Useful in cases where a connection cannot be automatically determined
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[
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9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/base.py#L100-L113
|
train
|
scottrice/pysteam
|
pysteam/_crc_algorithms.py
|
Crc.__get_nondirect_init
|
def __get_nondirect_init(self, init):
"""
return the non-direct init if the direct algorithm has been selected.
"""
crc = init
for i in range(self.Width):
bit = crc & 0x01
if bit:
crc^= self.Poly
crc >>= 1
if bit:
crc |= self.MSB_Mask
return crc & self.Mask
|
python
|
def __get_nondirect_init(self, init):
"""
return the non-direct init if the direct algorithm has been selected.
"""
crc = init
for i in range(self.Width):
bit = crc & 0x01
if bit:
crc^= self.Poly
crc >>= 1
if bit:
crc |= self.MSB_Mask
return crc & self.Mask
|
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return the non-direct init if the direct algorithm has been selected.
|
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1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L98-L110
|
train
|
scottrice/pysteam
|
pysteam/_crc_algorithms.py
|
Crc.reflect
|
def reflect(self, data, width):
"""
reflect a data word, i.e. reverts the bit order.
"""
x = data & 0x01
for i in range(width - 1):
data >>= 1
x = (x << 1) | (data & 0x01)
return x
|
python
|
def reflect(self, data, width):
"""
reflect a data word, i.e. reverts the bit order.
"""
x = data & 0x01
for i in range(width - 1):
data >>= 1
x = (x << 1) | (data & 0x01)
return x
|
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"return",
"x"
] |
reflect a data word, i.e. reverts the bit order.
|
[
"reflect",
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"data",
"word",
"i",
".",
"e",
".",
"reverts",
"the",
"bit",
"order",
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] |
1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L115-L123
|
train
|
scottrice/pysteam
|
pysteam/_crc_algorithms.py
|
Crc.bit_by_bit
|
def bit_by_bit(self, in_data):
"""
Classic simple and slow CRC implementation. This function iterates bit
by bit over the augmented input message and returns the calculated CRC
value at the end.
"""
# If the input data is a string, convert to bytes.
if isinstance(in_data, str):
in_data = [ord(c) for c in in_data]
register = self.NonDirectInit
for octet in in_data:
if self.ReflectIn:
octet = self.reflect(octet, 8)
for i in range(8):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask) | ((octet >> (7 - i)) & 0x01)
if topbit:
register ^= self.Poly
for i in range(self.Width):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask)
if topbit:
register ^= self.Poly
if self.ReflectOut:
register = self.reflect(register, self.Width)
return register ^ self.XorOut
|
python
|
def bit_by_bit(self, in_data):
"""
Classic simple and slow CRC implementation. This function iterates bit
by bit over the augmented input message and returns the calculated CRC
value at the end.
"""
# If the input data is a string, convert to bytes.
if isinstance(in_data, str):
in_data = [ord(c) for c in in_data]
register = self.NonDirectInit
for octet in in_data:
if self.ReflectIn:
octet = self.reflect(octet, 8)
for i in range(8):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask) | ((octet >> (7 - i)) & 0x01)
if topbit:
register ^= self.Poly
for i in range(self.Width):
topbit = register & self.MSB_Mask
register = ((register << 1) & self.Mask)
if topbit:
register ^= self.Poly
if self.ReflectOut:
register = self.reflect(register, self.Width)
return register ^ self.XorOut
|
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Classic simple and slow CRC implementation. This function iterates bit
by bit over the augmented input message and returns the calculated CRC
value at the end.
|
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1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L128-L156
|
train
|
scottrice/pysteam
|
pysteam/_crc_algorithms.py
|
Crc.gen_table
|
def gen_table(self):
"""
This function generates the CRC table used for the table_driven CRC
algorithm. The Python version cannot handle tables of an index width
other than 8. See the generated C code for tables with different sizes
instead.
"""
table_length = 1 << self.TableIdxWidth
tbl = [0] * table_length
for i in range(table_length):
register = i
if self.ReflectIn:
register = self.reflect(register, self.TableIdxWidth)
register = register << (self.Width - self.TableIdxWidth + self.CrcShift)
for j in range(self.TableIdxWidth):
if register & (self.MSB_Mask << self.CrcShift) != 0:
register = (register << 1) ^ (self.Poly << self.CrcShift)
else:
register = (register << 1)
if self.ReflectIn:
register = self.reflect(register >> self.CrcShift, self.Width) << self.CrcShift
tbl[i] = register & (self.Mask << self.CrcShift)
return tbl
|
python
|
def gen_table(self):
"""
This function generates the CRC table used for the table_driven CRC
algorithm. The Python version cannot handle tables of an index width
other than 8. See the generated C code for tables with different sizes
instead.
"""
table_length = 1 << self.TableIdxWidth
tbl = [0] * table_length
for i in range(table_length):
register = i
if self.ReflectIn:
register = self.reflect(register, self.TableIdxWidth)
register = register << (self.Width - self.TableIdxWidth + self.CrcShift)
for j in range(self.TableIdxWidth):
if register & (self.MSB_Mask << self.CrcShift) != 0:
register = (register << 1) ^ (self.Poly << self.CrcShift)
else:
register = (register << 1)
if self.ReflectIn:
register = self.reflect(register >> self.CrcShift, self.Width) << self.CrcShift
tbl[i] = register & (self.Mask << self.CrcShift)
return tbl
|
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] |
This function generates the CRC table used for the table_driven CRC
algorithm. The Python version cannot handle tables of an index width
other than 8. See the generated C code for tables with different sizes
instead.
|
[
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] |
1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L190-L212
|
train
|
scottrice/pysteam
|
pysteam/_crc_algorithms.py
|
Crc.table_driven
|
def table_driven(self, in_data):
"""
The Standard table_driven CRC algorithm.
"""
# If the input data is a string, convert to bytes.
if isinstance(in_data, str):
in_data = [ord(c) for c in in_data]
tbl = self.gen_table()
register = self.DirectInit << self.CrcShift
if not self.ReflectIn:
for octet in in_data:
tblidx = ((register >> (self.Width - self.TableIdxWidth + self.CrcShift)) ^ octet) & 0xff
register = ((register << (self.TableIdxWidth - self.CrcShift)) ^ tbl[tblidx]) & (self.Mask << self.CrcShift)
register = register >> self.CrcShift
else:
register = self.reflect(register, self.Width + self.CrcShift) << self.CrcShift
for octet in in_data:
tblidx = ((register >> self.CrcShift) ^ octet) & 0xff
register = ((register >> self.TableIdxWidth) ^ tbl[tblidx]) & (self.Mask << self.CrcShift)
register = self.reflect(register, self.Width + self.CrcShift) & self.Mask
if self.ReflectOut:
register = self.reflect(register, self.Width)
return register ^ self.XorOut
|
python
|
def table_driven(self, in_data):
"""
The Standard table_driven CRC algorithm.
"""
# If the input data is a string, convert to bytes.
if isinstance(in_data, str):
in_data = [ord(c) for c in in_data]
tbl = self.gen_table()
register = self.DirectInit << self.CrcShift
if not self.ReflectIn:
for octet in in_data:
tblidx = ((register >> (self.Width - self.TableIdxWidth + self.CrcShift)) ^ octet) & 0xff
register = ((register << (self.TableIdxWidth - self.CrcShift)) ^ tbl[tblidx]) & (self.Mask << self.CrcShift)
register = register >> self.CrcShift
else:
register = self.reflect(register, self.Width + self.CrcShift) << self.CrcShift
for octet in in_data:
tblidx = ((register >> self.CrcShift) ^ octet) & 0xff
register = ((register >> self.TableIdxWidth) ^ tbl[tblidx]) & (self.Mask << self.CrcShift)
register = self.reflect(register, self.Width + self.CrcShift) & self.Mask
if self.ReflectOut:
register = self.reflect(register, self.Width)
return register ^ self.XorOut
|
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The Standard table_driven CRC algorithm.
|
[
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] |
1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L217-L242
|
train
|
christophertbrown/bioscripts
|
ctbBio/strip_masked.py
|
parse_masked
|
def parse_masked(seq, min_len):
"""
parse masked sequence into non-masked and masked regions
"""
nm, masked = [], [[]]
prev = None
for base in seq[1]:
if base.isupper():
nm.append(base)
if masked != [[]] and len(masked[-1]) < min_len:
nm.extend(masked[-1])
del masked[-1]
prev = False
elif base.islower():
if prev is False:
masked.append([])
masked[-1].append(base)
prev = True
return nm, masked
|
python
|
def parse_masked(seq, min_len):
"""
parse masked sequence into non-masked and masked regions
"""
nm, masked = [], [[]]
prev = None
for base in seq[1]:
if base.isupper():
nm.append(base)
if masked != [[]] and len(masked[-1]) < min_len:
nm.extend(masked[-1])
del masked[-1]
prev = False
elif base.islower():
if prev is False:
masked.append([])
masked[-1].append(base)
prev = True
return nm, masked
|
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parse masked sequence into non-masked and masked regions
|
[
"parse",
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"and",
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] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_masked.py#L13-L31
|
train
|
christophertbrown/bioscripts
|
ctbBio/strip_masked.py
|
strip_masked
|
def strip_masked(fasta, min_len, print_masked):
"""
remove masked regions from fasta file as long as
they are longer than min_len
"""
for seq in parse_fasta(fasta):
nm, masked = parse_masked(seq, min_len)
nm = ['%s removed_masked >=%s' % (seq[0], min_len), ''.join(nm)]
yield [0, nm]
if print_masked is True:
for i, m in enumerate([i for i in masked if i != []], 1):
m = ['%s insertion:%s' % (seq[0], i), ''.join(m)]
yield [1, m]
|
python
|
def strip_masked(fasta, min_len, print_masked):
"""
remove masked regions from fasta file as long as
they are longer than min_len
"""
for seq in parse_fasta(fasta):
nm, masked = parse_masked(seq, min_len)
nm = ['%s removed_masked >=%s' % (seq[0], min_len), ''.join(nm)]
yield [0, nm]
if print_masked is True:
for i, m in enumerate([i for i in masked if i != []], 1):
m = ['%s insertion:%s' % (seq[0], i), ''.join(m)]
yield [1, m]
|
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remove masked regions from fasta file as long as
they are longer than min_len
|
[
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"fasta",
"file",
"as",
"long",
"as",
"they",
"are",
"longer",
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"min_len"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_masked.py#L33-L45
|
train
|
smdabdoub/phylotoast
|
bin/network_plots_gephi.py
|
get_relative_abundance
|
def get_relative_abundance(biomfile):
"""
Return arcsine transformed relative abundance from a BIOM format file.
:type biomfile: BIOM format file
:param biomfile: BIOM format file used to obtain relative abundances for each OTU in
a SampleID, which are used as node sizes in network plots.
:type return: Dictionary of dictionaries.
:return: Dictionary keyed on SampleID whose value is a dictionarykeyed on OTU Name
whose value is the arc sine tranfsormed relative abundance value for that
SampleID-OTU Name pair.
"""
biomf = biom.load_table(biomfile)
norm_biomf = biomf.norm(inplace=False)
rel_abd = {}
for sid in norm_biomf.ids():
rel_abd[sid] = {}
for otuid in norm_biomf.ids("observation"):
otuname = oc.otu_name(norm_biomf.metadata(otuid, axis="observation")["taxonomy"])
otuname = " ".join(otuname.split("_"))
abd = norm_biomf.get_value_by_ids(otuid, sid)
rel_abd[sid][otuname] = abd
ast_rel_abd = bc.arcsine_sqrt_transform(rel_abd)
return ast_rel_abd
|
python
|
def get_relative_abundance(biomfile):
"""
Return arcsine transformed relative abundance from a BIOM format file.
:type biomfile: BIOM format file
:param biomfile: BIOM format file used to obtain relative abundances for each OTU in
a SampleID, which are used as node sizes in network plots.
:type return: Dictionary of dictionaries.
:return: Dictionary keyed on SampleID whose value is a dictionarykeyed on OTU Name
whose value is the arc sine tranfsormed relative abundance value for that
SampleID-OTU Name pair.
"""
biomf = biom.load_table(biomfile)
norm_biomf = biomf.norm(inplace=False)
rel_abd = {}
for sid in norm_biomf.ids():
rel_abd[sid] = {}
for otuid in norm_biomf.ids("observation"):
otuname = oc.otu_name(norm_biomf.metadata(otuid, axis="observation")["taxonomy"])
otuname = " ".join(otuname.split("_"))
abd = norm_biomf.get_value_by_ids(otuid, sid)
rel_abd[sid][otuname] = abd
ast_rel_abd = bc.arcsine_sqrt_transform(rel_abd)
return ast_rel_abd
|
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Return arcsine transformed relative abundance from a BIOM format file.
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a SampleID, which are used as node sizes in network plots.
:type return: Dictionary of dictionaries.
:return: Dictionary keyed on SampleID whose value is a dictionarykeyed on OTU Name
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[
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"relative",
"abundance",
"from",
"a",
"BIOM",
"format",
"file",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/network_plots_gephi.py#L33-L57
|
train
|
smdabdoub/phylotoast
|
bin/iTol.py
|
find_otu
|
def find_otu(otuid, tree):
"""
Find an OTU ID in a Newick-format tree.
Return the starting position of the ID or None if not found.
"""
for m in re.finditer(otuid, tree):
before, after = tree[m.start()-1], tree[m.start()+len(otuid)]
if before in ["(", ",", ")"] and after in [":", ";"]:
return m.start()
return None
|
python
|
def find_otu(otuid, tree):
"""
Find an OTU ID in a Newick-format tree.
Return the starting position of the ID or None if not found.
"""
for m in re.finditer(otuid, tree):
before, after = tree[m.start()-1], tree[m.start()+len(otuid)]
if before in ["(", ",", ")"] and after in [":", ";"]:
return m.start()
return None
|
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Find an OTU ID in a Newick-format tree.
Return the starting position of the ID or None if not found.
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] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/iTol.py#L17-L26
|
train
|
smdabdoub/phylotoast
|
bin/iTol.py
|
newick_replace_otuids
|
def newick_replace_otuids(tree, biomf):
"""
Replace the OTU ids in the Newick phylogenetic tree format with truncated
OTU names
"""
for val, id_, md in biomf.iter(axis="observation"):
otu_loc = find_otu(id_, tree)
if otu_loc is not None:
tree = tree[:otu_loc] + \
oc.otu_name(md["taxonomy"]) + \
tree[otu_loc + len(id_):]
return tree
|
python
|
def newick_replace_otuids(tree, biomf):
"""
Replace the OTU ids in the Newick phylogenetic tree format with truncated
OTU names
"""
for val, id_, md in biomf.iter(axis="observation"):
otu_loc = find_otu(id_, tree)
if otu_loc is not None:
tree = tree[:otu_loc] + \
oc.otu_name(md["taxonomy"]) + \
tree[otu_loc + len(id_):]
return tree
|
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Replace the OTU ids in the Newick phylogenetic tree format with truncated
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"Newick",
"phylogenetic",
"tree",
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"with",
"truncated",
"OTU",
"names"
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/iTol.py#L29-L40
|
train
|
christophertbrown/bioscripts
|
ctbBio/cluster_ani.py
|
genome_info
|
def genome_info(genome, info):
"""
return genome info for choosing representative
if ggKbase table provided - choose rep based on SCGs and genome length
- priority for most SCGs - extra SCGs, then largest genome
otherwise, based on largest genome
"""
try:
scg = info['#SCGs']
dups = info['#SCG duplicates']
length = info['genome size (bp)']
return [scg - dups, length, genome]
except:
return [False, False, info['genome size (bp)'], genome]
|
python
|
def genome_info(genome, info):
"""
return genome info for choosing representative
if ggKbase table provided - choose rep based on SCGs and genome length
- priority for most SCGs - extra SCGs, then largest genome
otherwise, based on largest genome
"""
try:
scg = info['#SCGs']
dups = info['#SCG duplicates']
length = info['genome size (bp)']
return [scg - dups, length, genome]
except:
return [False, False, info['genome size (bp)'], genome]
|
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return genome info for choosing representative
if ggKbase table provided - choose rep based on SCGs and genome length
- priority for most SCGs - extra SCGs, then largest genome
otherwise, based on largest genome
|
[
"return",
"genome",
"info",
"for",
"choosing",
"representative"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L97-L112
|
train
|
christophertbrown/bioscripts
|
ctbBio/cluster_ani.py
|
print_clusters
|
def print_clusters(fastas, info, ANI):
"""
choose represenative genome and
print cluster information
*if ggKbase table is provided, use SCG info to choose best genome
"""
header = ['#cluster', 'num. genomes', 'rep.', 'genome', '#SCGs', '#SCG duplicates', \
'genome size (bp)', 'fragments', 'list']
yield header
in_cluster = []
for cluster_num, cluster in enumerate(connected_components(ANI)):
cluster = sorted([genome_info(genome, info[genome]) \
for genome in cluster], \
key = lambda x: x[0:], reverse = True)
rep = cluster[0][-1]
cluster = [i[-1] for i in cluster]
size = len(cluster)
for genome in cluster:
in_cluster.append(genome)
try:
stats = [size, rep, genome, \
info[genome]['#SCGs'], info[genome]['#SCG duplicates'], \
info[genome]['genome size (bp)'], info[genome]['# contigs'], cluster]
except:
stats = [size, rep, genome, \
'n/a', 'n/a', \
info[genome]['genome size (bp)'], info[genome]['# contigs'], cluster]
if rep == genome:
stats = ['*%s' % (cluster_num)] + stats
else:
stats = [cluster_num] + stats
yield stats
# print singletons
try:
start = cluster_num + 1
except:
start = 0
fastas = set([i.rsplit('.', 1)[0].rsplit('/', 1)[-1].rsplit('.contigs')[0] for i in fastas])
for cluster_num, genome in \
enumerate(fastas.difference(set(in_cluster)), start):
try:
stats = ['*%s' % (cluster_num), 1, genome, genome, \
info[genome]['#SCGs'], info[genome]['#SCG duplicates'], \
info[genome]['genome size (bp)'], info[genome]['# contigs'], [genome]]
except:
stats = ['*%s' % (cluster_num), 1, genome, genome, \
'n/a', 'n/a', \
info[genome]['genome size (bp)'], info[genome]['# contigs'], [genome]]
yield stats
|
python
|
def print_clusters(fastas, info, ANI):
"""
choose represenative genome and
print cluster information
*if ggKbase table is provided, use SCG info to choose best genome
"""
header = ['#cluster', 'num. genomes', 'rep.', 'genome', '#SCGs', '#SCG duplicates', \
'genome size (bp)', 'fragments', 'list']
yield header
in_cluster = []
for cluster_num, cluster in enumerate(connected_components(ANI)):
cluster = sorted([genome_info(genome, info[genome]) \
for genome in cluster], \
key = lambda x: x[0:], reverse = True)
rep = cluster[0][-1]
cluster = [i[-1] for i in cluster]
size = len(cluster)
for genome in cluster:
in_cluster.append(genome)
try:
stats = [size, rep, genome, \
info[genome]['#SCGs'], info[genome]['#SCG duplicates'], \
info[genome]['genome size (bp)'], info[genome]['# contigs'], cluster]
except:
stats = [size, rep, genome, \
'n/a', 'n/a', \
info[genome]['genome size (bp)'], info[genome]['# contigs'], cluster]
if rep == genome:
stats = ['*%s' % (cluster_num)] + stats
else:
stats = [cluster_num] + stats
yield stats
# print singletons
try:
start = cluster_num + 1
except:
start = 0
fastas = set([i.rsplit('.', 1)[0].rsplit('/', 1)[-1].rsplit('.contigs')[0] for i in fastas])
for cluster_num, genome in \
enumerate(fastas.difference(set(in_cluster)), start):
try:
stats = ['*%s' % (cluster_num), 1, genome, genome, \
info[genome]['#SCGs'], info[genome]['#SCG duplicates'], \
info[genome]['genome size (bp)'], info[genome]['# contigs'], [genome]]
except:
stats = ['*%s' % (cluster_num), 1, genome, genome, \
'n/a', 'n/a', \
info[genome]['genome size (bp)'], info[genome]['# contigs'], [genome]]
yield stats
|
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choose represenative genome and
print cluster information
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|
[
"choose",
"represenative",
"genome",
"and",
"print",
"cluster",
"information"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L114-L163
|
train
|
christophertbrown/bioscripts
|
ctbBio/cluster_ani.py
|
parse_ggKbase_tables
|
def parse_ggKbase_tables(tables, id_type):
"""
convert ggKbase genome info tables to dictionary
"""
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('name'):
header = line
header[4] = 'genome size (bp)'
header[12] = '#SCGs'
header[13] = '#SCG duplicates'
continue
name, code, info = line[0], line[1], line
info = [to_int(i) for i in info]
if id_type is False: # try to use name and code ID
if 'UNK' in code or 'unknown' in code:
code = name
if (name != code) and (name and code in g2info):
print('# duplicate name or code in table(s)', file=sys.stderr)
print('# %s and/or %s' % (name, code), file=sys.stderr)
exit()
if name not in g2info:
g2info[name] = {item:stat for item, stat in zip(header, info)}
if code not in g2info:
g2info[code] = {item:stat for item, stat in zip(header, info)}
else:
if id_type == 'name':
ID = name
elif id_type == 'code':
ID = code
else:
print('# specify name or code column using -id', file=sys.stderr)
exit()
ID = ID.replace(' ', '')
g2info[ID] = {item:stat for item, stat in zip(header, info)}
if g2info[ID]['genome size (bp)'] == '':
g2info[ID]['genome size (bp)'] = 0
return g2info
|
python
|
def parse_ggKbase_tables(tables, id_type):
"""
convert ggKbase genome info tables to dictionary
"""
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('name'):
header = line
header[4] = 'genome size (bp)'
header[12] = '#SCGs'
header[13] = '#SCG duplicates'
continue
name, code, info = line[0], line[1], line
info = [to_int(i) for i in info]
if id_type is False: # try to use name and code ID
if 'UNK' in code or 'unknown' in code:
code = name
if (name != code) and (name and code in g2info):
print('# duplicate name or code in table(s)', file=sys.stderr)
print('# %s and/or %s' % (name, code), file=sys.stderr)
exit()
if name not in g2info:
g2info[name] = {item:stat for item, stat in zip(header, info)}
if code not in g2info:
g2info[code] = {item:stat for item, stat in zip(header, info)}
else:
if id_type == 'name':
ID = name
elif id_type == 'code':
ID = code
else:
print('# specify name or code column using -id', file=sys.stderr)
exit()
ID = ID.replace(' ', '')
g2info[ID] = {item:stat for item, stat in zip(header, info)}
if g2info[ID]['genome size (bp)'] == '':
g2info[ID]['genome size (bp)'] = 0
return g2info
|
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convert ggKbase genome info tables to dictionary
|
[
"convert",
"ggKbase",
"genome",
"info",
"tables",
"to",
"dictionary"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L174-L213
|
train
|
christophertbrown/bioscripts
|
ctbBio/cluster_ani.py
|
parse_checkM_tables
|
def parse_checkM_tables(tables):
"""
convert checkM genome info tables to dictionary
"""
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('Bin Id'):
header = line
header[8] = 'genome size (bp)'
header[5] = '#SCGs'
header[6] = '#SCG duplicates'
continue
ID, info = line[0], line
info = [to_int(i) for i in info]
ID = ID.replace(' ', '')
g2info[ID] = {item:stat for item, stat in zip(header, info)}
if g2info[ID]['genome size (bp)'] == '':
g2info[ID]['genome size (bp)'] = 0
return g2info
|
python
|
def parse_checkM_tables(tables):
"""
convert checkM genome info tables to dictionary
"""
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('Bin Id'):
header = line
header[8] = 'genome size (bp)'
header[5] = '#SCGs'
header[6] = '#SCG duplicates'
continue
ID, info = line[0], line
info = [to_int(i) for i in info]
ID = ID.replace(' ', '')
g2info[ID] = {item:stat for item, stat in zip(header, info)}
if g2info[ID]['genome size (bp)'] == '':
g2info[ID]['genome size (bp)'] = 0
return g2info
|
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convert checkM genome info tables to dictionary
|
[
"convert",
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"genome",
"info",
"tables",
"to",
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] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L215-L235
|
train
|
christophertbrown/bioscripts
|
ctbBio/cluster_ani.py
|
genome_lengths
|
def genome_lengths(fastas, info):
"""
get genome lengths
"""
if info is False:
info = {}
for genome in fastas:
name = genome.rsplit('.', 1)[0].rsplit('/', 1)[-1].rsplit('.contigs')[0]
if name in info:
continue
length = 0
fragments = 0
for seq in parse_fasta(genome):
length += len(seq[1])
fragments += 1
info[name] = {'genome size (bp)':length, '# contigs':fragments}
return info
|
python
|
def genome_lengths(fastas, info):
"""
get genome lengths
"""
if info is False:
info = {}
for genome in fastas:
name = genome.rsplit('.', 1)[0].rsplit('/', 1)[-1].rsplit('.contigs')[0]
if name in info:
continue
length = 0
fragments = 0
for seq in parse_fasta(genome):
length += len(seq[1])
fragments += 1
info[name] = {'genome size (bp)':length, '# contigs':fragments}
return info
|
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get genome lengths
|
[
"get",
"genome",
"lengths"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L237-L253
|
train
|
disqus/nydus
|
nydus/db/routers/base.py
|
BaseRouter.get_dbs
|
def get_dbs(self, attr, args, kwargs, **fkwargs):
"""
Returns a list of db keys to route the given call to.
:param attr: Name of attribute being called on the connection.
:param args: List of arguments being passed to ``attr``.
:param kwargs: Dictionary of keyword arguments being passed to ``attr``.
>>> redis = Cluster(router=BaseRouter)
>>> router = redis.router
>>> router.get_dbs('incr', args=('key name', 1))
[0,1,2]
"""
if not self._ready:
if not self.setup_router(args=args, kwargs=kwargs, **fkwargs):
raise self.UnableToSetupRouter()
retval = self._pre_routing(attr=attr, args=args, kwargs=kwargs, **fkwargs)
if retval is not None:
args, kwargs = retval
if not (args or kwargs):
return self.cluster.hosts.keys()
try:
db_nums = self._route(attr=attr, args=args, kwargs=kwargs, **fkwargs)
except Exception as e:
self._handle_exception(e)
db_nums = []
return self._post_routing(attr=attr, db_nums=db_nums, args=args, kwargs=kwargs, **fkwargs)
|
python
|
def get_dbs(self, attr, args, kwargs, **fkwargs):
"""
Returns a list of db keys to route the given call to.
:param attr: Name of attribute being called on the connection.
:param args: List of arguments being passed to ``attr``.
:param kwargs: Dictionary of keyword arguments being passed to ``attr``.
>>> redis = Cluster(router=BaseRouter)
>>> router = redis.router
>>> router.get_dbs('incr', args=('key name', 1))
[0,1,2]
"""
if not self._ready:
if not self.setup_router(args=args, kwargs=kwargs, **fkwargs):
raise self.UnableToSetupRouter()
retval = self._pre_routing(attr=attr, args=args, kwargs=kwargs, **fkwargs)
if retval is not None:
args, kwargs = retval
if not (args or kwargs):
return self.cluster.hosts.keys()
try:
db_nums = self._route(attr=attr, args=args, kwargs=kwargs, **fkwargs)
except Exception as e:
self._handle_exception(e)
db_nums = []
return self._post_routing(attr=attr, db_nums=db_nums, args=args, kwargs=kwargs, **fkwargs)
|
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:param kwargs: Dictionary of keyword arguments being passed to ``attr``.
>>> redis = Cluster(router=BaseRouter)
>>> router = redis.router
>>> router.get_dbs('incr', args=('key name', 1))
[0,1,2]
|
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] |
9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L50-L81
|
train
|
disqus/nydus
|
nydus/db/routers/base.py
|
BaseRouter.setup_router
|
def setup_router(self, args, kwargs, **fkwargs):
"""
Call method to perform any setup
"""
self._ready = self._setup_router(args=args, kwargs=kwargs, **fkwargs)
return self._ready
|
python
|
def setup_router(self, args, kwargs, **fkwargs):
"""
Call method to perform any setup
"""
self._ready = self._setup_router(args=args, kwargs=kwargs, **fkwargs)
return self._ready
|
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Call method to perform any setup
|
[
"Call",
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"any",
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9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L87-L93
|
train
|
disqus/nydus
|
nydus/db/routers/base.py
|
BaseRouter._route
|
def _route(self, attr, args, kwargs, **fkwargs):
"""
Perform routing and return db_nums
"""
return self.cluster.hosts.keys()
|
python
|
def _route(self, attr, args, kwargs, **fkwargs):
"""
Perform routing and return db_nums
"""
return self.cluster.hosts.keys()
|
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Perform routing and return db_nums
|
[
"Perform",
"routing",
"and",
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"db_nums"
] |
9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L111-L115
|
train
|
disqus/nydus
|
nydus/db/routers/base.py
|
RoundRobinRouter.check_down_connections
|
def check_down_connections(self):
"""
Iterates through all connections which were previously listed as unavailable
and marks any that have expired their retry_timeout as being up.
"""
now = time.time()
for db_num, marked_down_at in self._down_connections.items():
if marked_down_at + self.retry_timeout <= now:
self.mark_connection_up(db_num)
|
python
|
def check_down_connections(self):
"""
Iterates through all connections which were previously listed as unavailable
and marks any that have expired their retry_timeout as being up.
"""
now = time.time()
for db_num, marked_down_at in self._down_connections.items():
if marked_down_at + self.retry_timeout <= now:
self.mark_connection_up(db_num)
|
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9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L175-L184
|
train
|
disqus/nydus
|
nydus/db/routers/base.py
|
RoundRobinRouter.flush_down_connections
|
def flush_down_connections(self):
"""
Marks all connections which were previously listed as unavailable as being up.
"""
self._get_db_attempts = 0
for db_num in self._down_connections.keys():
self.mark_connection_up(db_num)
|
python
|
def flush_down_connections(self):
"""
Marks all connections which were previously listed as unavailable as being up.
"""
self._get_db_attempts = 0
for db_num in self._down_connections.keys():
self.mark_connection_up(db_num)
|
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"unavailable",
"as",
"being",
"up",
"."
] |
9b505840da47a34f758a830c3992fa5dcb7bb7ad
|
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L186-L192
|
train
|
opengridcc/opengrid
|
opengrid/library/analysis.py
|
standby
|
def standby(df, resolution='24h', time_window=None):
"""
Compute standby power
Parameters
----------
df : pandas.DataFrame or pandas.Series
Electricity Power
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
df : pandas.Series with DateTimeIndex in the given resolution
"""
if df.empty:
raise EmptyDataFrame()
df = pd.DataFrame(df) # if df was a pd.Series, convert to DataFrame
def parse_time(t):
if isinstance(t, numbers.Number):
return pd.Timestamp.utcfromtimestamp(t).time()
else:
return pd.Timestamp(t).time()
# first filter based on the time-window
if time_window is not None:
t_start = parse_time(time_window[0])
t_end = parse_time(time_window[1])
if t_start > t_end:
# start before midnight
df = df[(df.index.time >= t_start) | (df.index.time < t_end)]
else:
df = df[(df.index.time >= t_start) & (df.index.time < t_end)]
return df.resample(resolution).min()
|
python
|
def standby(df, resolution='24h', time_window=None):
"""
Compute standby power
Parameters
----------
df : pandas.DataFrame or pandas.Series
Electricity Power
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
df : pandas.Series with DateTimeIndex in the given resolution
"""
if df.empty:
raise EmptyDataFrame()
df = pd.DataFrame(df) # if df was a pd.Series, convert to DataFrame
def parse_time(t):
if isinstance(t, numbers.Number):
return pd.Timestamp.utcfromtimestamp(t).time()
else:
return pd.Timestamp(t).time()
# first filter based on the time-window
if time_window is not None:
t_start = parse_time(time_window[0])
t_end = parse_time(time_window[1])
if t_start > t_end:
# start before midnight
df = df[(df.index.time >= t_start) | (df.index.time < t_end)]
else:
df = df[(df.index.time >= t_start) & (df.index.time < t_end)]
return df.resample(resolution).min()
|
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Compute standby power
Parameters
----------
df : pandas.DataFrame or pandas.Series
Electricity Power
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
df : pandas.Series with DateTimeIndex in the given resolution
|
[
"Compute",
"standby",
"power"
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L72-L115
|
train
|
opengridcc/opengrid
|
opengrid/library/analysis.py
|
share_of_standby
|
def share_of_standby(df, resolution='24h', time_window=None):
"""
Compute the share of the standby power in the total consumption.
Parameters
----------
df : pandas.DataFrame or pandas.Series
Power (typically electricity, can be anything)
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
fraction : float between 0-1 with the share of the standby consumption
"""
p_sb = standby(df, resolution, time_window)
df = df.resample(resolution).mean()
p_tot = df.sum()
p_standby = p_sb.sum()
share_standby = p_standby / p_tot
res = share_standby.iloc[0]
return res
|
python
|
def share_of_standby(df, resolution='24h', time_window=None):
"""
Compute the share of the standby power in the total consumption.
Parameters
----------
df : pandas.DataFrame or pandas.Series
Power (typically electricity, can be anything)
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
fraction : float between 0-1 with the share of the standby consumption
"""
p_sb = standby(df, resolution, time_window)
df = df.resample(resolution).mean()
p_tot = df.sum()
p_standby = p_sb.sum()
share_standby = p_standby / p_tot
res = share_standby.iloc[0]
return res
|
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Compute the share of the standby power in the total consumption.
Parameters
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df : pandas.DataFrame or pandas.Series
Power (typically electricity, can be anything)
resolution : str, default='d'
Resolution of the computation. Data will be resampled to this resolution (as mean) before computation
of the minimum.
String that can be parsed by the pandas resample function, example ='h', '15min', '6h'
time_window : tuple with start-hour and end-hour, default=None
Specify the start-time and end-time for the analysis.
Only data within this time window will be considered.
Both times have to be specified as string ('01:00', '06:30') or as datetime.time() objects
Returns
-------
fraction : float between 0-1 with the share of the standby consumption
|
[
"Compute",
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"share",
"of",
"the",
"standby",
"power",
"in",
"the",
"total",
"consumption",
"."
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L118-L146
|
train
|
opengridcc/opengrid
|
opengrid/library/analysis.py
|
count_peaks
|
def count_peaks(ts):
"""
Toggle counter for gas boilers
Counts the number of times the gas consumption increases with more than 3kW
Parameters
----------
ts: Pandas Series
Gas consumption in minute resolution
Returns
-------
int
"""
on_toggles = ts.diff() > 3000
shifted = np.logical_not(on_toggles.shift(1))
result = on_toggles & shifted
count = result.sum()
return count
|
python
|
def count_peaks(ts):
"""
Toggle counter for gas boilers
Counts the number of times the gas consumption increases with more than 3kW
Parameters
----------
ts: Pandas Series
Gas consumption in minute resolution
Returns
-------
int
"""
on_toggles = ts.diff() > 3000
shifted = np.logical_not(on_toggles.shift(1))
result = on_toggles & shifted
count = result.sum()
return count
|
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Toggle counter for gas boilers
Counts the number of times the gas consumption increases with more than 3kW
Parameters
----------
ts: Pandas Series
Gas consumption in minute resolution
Returns
-------
int
|
[
"Toggle",
"counter",
"for",
"gas",
"boilers"
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L149-L169
|
train
|
opengridcc/opengrid
|
opengrid/library/analysis.py
|
load_factor
|
def load_factor(ts, resolution=None, norm=None):
"""
Calculate the ratio of input vs. norm over a given interval.
Parameters
----------
ts : pandas.Series
timeseries
resolution : str, optional
interval over which to calculate the ratio
default: resolution of the input timeseries
norm : int | float, optional
denominator of the ratio
default: the maximum of the input timeseries
Returns
-------
pandas.Series
"""
if norm is None:
norm = ts.max()
if resolution is not None:
ts = ts.resample(rule=resolution).mean()
lf = ts / norm
return lf
|
python
|
def load_factor(ts, resolution=None, norm=None):
"""
Calculate the ratio of input vs. norm over a given interval.
Parameters
----------
ts : pandas.Series
timeseries
resolution : str, optional
interval over which to calculate the ratio
default: resolution of the input timeseries
norm : int | float, optional
denominator of the ratio
default: the maximum of the input timeseries
Returns
-------
pandas.Series
"""
if norm is None:
norm = ts.max()
if resolution is not None:
ts = ts.resample(rule=resolution).mean()
lf = ts / norm
return lf
|
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Calculate the ratio of input vs. norm over a given interval.
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ts : pandas.Series
timeseries
resolution : str, optional
interval over which to calculate the ratio
default: resolution of the input timeseries
norm : int | float, optional
denominator of the ratio
default: the maximum of the input timeseries
Returns
-------
pandas.Series
|
[
"Calculate",
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"vs",
".",
"norm",
"over",
"a",
"given",
"interval",
"."
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L172-L199
|
train
|
christophertbrown/bioscripts
|
ctbBio/besthits.py
|
top_hits
|
def top_hits(hits, num, column, reverse):
"""
get top hits after sorting by column number
"""
hits.sort(key = itemgetter(column), reverse = reverse)
for hit in hits[0:num]:
yield hit
|
python
|
def top_hits(hits, num, column, reverse):
"""
get top hits after sorting by column number
"""
hits.sort(key = itemgetter(column), reverse = reverse)
for hit in hits[0:num]:
yield hit
|
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get top hits after sorting by column number
|
[
"get",
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"after",
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"by",
"column",
"number"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L17-L23
|
train
|
christophertbrown/bioscripts
|
ctbBio/besthits.py
|
numBlast_sort
|
def numBlast_sort(blast, numHits, evalueT, bitT):
"""
parse b6 output with sorting
"""
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
hmm = {h:[] for h in header}
for line in blast:
if line.startswith('#'):
continue
line = line.strip().split('\t')
# Evalue and Bitscore thresholds
line[10], line[11] = float(line[10]), float(line[11])
evalue, bit = line[10], line[11]
if evalueT is not False and evalue > evalueT:
continue
if bitT is not False and bit < bitT:
continue
for i, h in zip(line, header):
hmm[h].append(i)
hmm = pd.DataFrame(hmm)
for query, df in hmm.groupby(by = ['#query']):
df = df.sort_values(by = ['bitscore'], ascending = False)
for hit in df[header].values[0:numHits]:
yield hit
|
python
|
def numBlast_sort(blast, numHits, evalueT, bitT):
"""
parse b6 output with sorting
"""
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
hmm = {h:[] for h in header}
for line in blast:
if line.startswith('#'):
continue
line = line.strip().split('\t')
# Evalue and Bitscore thresholds
line[10], line[11] = float(line[10]), float(line[11])
evalue, bit = line[10], line[11]
if evalueT is not False and evalue > evalueT:
continue
if bitT is not False and bit < bitT:
continue
for i, h in zip(line, header):
hmm[h].append(i)
hmm = pd.DataFrame(hmm)
for query, df in hmm.groupby(by = ['#query']):
df = df.sort_values(by = ['bitscore'], ascending = False)
for hit in df[header].values[0:numHits]:
yield hit
|
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parse b6 output with sorting
|
[
"parse",
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] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L25-L50
|
train
|
christophertbrown/bioscripts
|
ctbBio/besthits.py
|
numBlast
|
def numBlast(blast, numHits, evalueT = False, bitT = False, sort = False):
"""
parse b6 output
"""
if sort is True:
for hit in numBlast_sort(blast, numHits, evalueT, bitT):
yield hit
return
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
prev, hits = None, []
for line in blast:
line = line.strip().split('\t')
ID = line[0]
line[10], line[11] = float(line[10]), float(line[11])
evalue, bit = line[10], line[11]
if ID != prev:
if len(hits) > 0:
# column is 1 + line index
for hit in top_hits(hits, numHits, 11, True):
yield hit
hits = []
if evalueT == False and bitT == False:
hits.append(line)
elif evalue <= evalueT and bitT == False:
hits.append(line)
elif evalue <= evalueT and bit >= bitT:
hits.append(line)
elif evalueT == False and bit >= bitT:
hits.append(line)
prev = ID
for hit in top_hits(hits, numHits, 11, True):
yield hit
|
python
|
def numBlast(blast, numHits, evalueT = False, bitT = False, sort = False):
"""
parse b6 output
"""
if sort is True:
for hit in numBlast_sort(blast, numHits, evalueT, bitT):
yield hit
return
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
prev, hits = None, []
for line in blast:
line = line.strip().split('\t')
ID = line[0]
line[10], line[11] = float(line[10]), float(line[11])
evalue, bit = line[10], line[11]
if ID != prev:
if len(hits) > 0:
# column is 1 + line index
for hit in top_hits(hits, numHits, 11, True):
yield hit
hits = []
if evalueT == False and bitT == False:
hits.append(line)
elif evalue <= evalueT and bitT == False:
hits.append(line)
elif evalue <= evalueT and bit >= bitT:
hits.append(line)
elif evalueT == False and bit >= bitT:
hits.append(line)
prev = ID
for hit in top_hits(hits, numHits, 11, True):
yield hit
|
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parse b6 output
|
[
"parse",
"b6",
"output"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L52-L85
|
train
|
christophertbrown/bioscripts
|
ctbBio/besthits.py
|
numDomtblout
|
def numDomtblout(domtblout, numHits, evalueT, bitT, sort):
"""
parse hmm domain table output
this version is faster but does not work unless the table is sorted
"""
if sort is True:
for hit in numDomtblout_sort(domtblout, numHits, evalueT, bitT):
yield hit
return
header = ['#target name', 'target accession', 'tlen',
'query name', 'query accession', 'qlen',
'full E-value', 'full score', 'full bias',
'domain #', '# domains',
'domain c-Evalue', 'domain i-Evalue', 'domain score', 'domain bias',
'hmm from', 'hmm to', 'seq from', 'seq to', 'env from', 'env to',
'acc', 'target description']
yield header
prev, hits = None, []
for line in domtblout:
if line.startswith('#'):
continue
# parse line and get description
line = line.strip().split()
desc = ' '.join(line[18:])
line = line[0:18]
line.append(desc)
# create ID based on query name and domain number
ID = line[0] + line[9]
# domain c-Evalue and domain score thresholds
line[11], line[13] = float(line[11]), float(line[13])
evalue, bitscore = line[11], line[13]
line[11], line[13] = evalue, bitscore
if ID != prev:
if len(hits) > 0:
for hit in top_hits(hits, numHits, 13, True):
yield hit
hits = []
if evalueT == False and bitT == False:
hits.append(line)
elif evalue <= evalueT and bitT == False:
hits.append(line)
elif evalue <= evalueT and bit >= bitT:
hits.append(line)
elif evalueT == False and bit >= bitT:
hits.append(line)
prev = ID
for hit in top_hits(hits, numHits, 13, True):
yield hit
|
python
|
def numDomtblout(domtblout, numHits, evalueT, bitT, sort):
"""
parse hmm domain table output
this version is faster but does not work unless the table is sorted
"""
if sort is True:
for hit in numDomtblout_sort(domtblout, numHits, evalueT, bitT):
yield hit
return
header = ['#target name', 'target accession', 'tlen',
'query name', 'query accession', 'qlen',
'full E-value', 'full score', 'full bias',
'domain #', '# domains',
'domain c-Evalue', 'domain i-Evalue', 'domain score', 'domain bias',
'hmm from', 'hmm to', 'seq from', 'seq to', 'env from', 'env to',
'acc', 'target description']
yield header
prev, hits = None, []
for line in domtblout:
if line.startswith('#'):
continue
# parse line and get description
line = line.strip().split()
desc = ' '.join(line[18:])
line = line[0:18]
line.append(desc)
# create ID based on query name and domain number
ID = line[0] + line[9]
# domain c-Evalue and domain score thresholds
line[11], line[13] = float(line[11]), float(line[13])
evalue, bitscore = line[11], line[13]
line[11], line[13] = evalue, bitscore
if ID != prev:
if len(hits) > 0:
for hit in top_hits(hits, numHits, 13, True):
yield hit
hits = []
if evalueT == False and bitT == False:
hits.append(line)
elif evalue <= evalueT and bitT == False:
hits.append(line)
elif evalue <= evalueT and bit >= bitT:
hits.append(line)
elif evalueT == False and bit >= bitT:
hits.append(line)
prev = ID
for hit in top_hits(hits, numHits, 13, True):
yield hit
|
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parse hmm domain table output
this version is faster but does not work unless the table is sorted
|
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83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L121-L168
|
train
|
christophertbrown/bioscripts
|
ctbBio/stockholm2fa.py
|
stock2fa
|
def stock2fa(stock):
"""
convert stockholm to fasta
"""
seqs = {}
for line in stock:
if line.startswith('#') is False and line.startswith(' ') is False and len(line) > 3:
id, seq = line.strip().split()
id = id.rsplit('/', 1)[0]
id = re.split('[0-9]\|', id, 1)[-1]
if id not in seqs:
seqs[id] = []
seqs[id].append(seq)
if line.startswith('//'):
break
return seqs
|
python
|
def stock2fa(stock):
"""
convert stockholm to fasta
"""
seqs = {}
for line in stock:
if line.startswith('#') is False and line.startswith(' ') is False and len(line) > 3:
id, seq = line.strip().split()
id = id.rsplit('/', 1)[0]
id = re.split('[0-9]\|', id, 1)[-1]
if id not in seqs:
seqs[id] = []
seqs[id].append(seq)
if line.startswith('//'):
break
return seqs
|
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convert stockholm to fasta
|
[
"convert",
"stockholm",
"to",
"fasta"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2fa.py#L11-L26
|
train
|
opengridcc/opengrid
|
opengrid/library/utils.py
|
week_schedule
|
def week_schedule(index, on_time=None, off_time=None, off_days=None):
""" Return boolean time series following given week schedule.
Parameters
----------
index : pandas.DatetimeIndex
Datetime index
on_time : str or datetime.time
Daily opening time. Default: '09:00'
off_time : str or datetime.time
Daily closing time. Default: '17:00'
off_days : list of str
List of weekdays. Default: ['Sunday', 'Monday']
Returns
-------
pandas.Series of bool
True when on, False otherwise for given datetime index
Examples
--------
>>> import pandas as pd
>>> from opengrid.library.utils import week_schedule
>>> index = pd.date_range('20170701', '20170710', freq='H')
>>> week_schedule(index)
"""
if on_time is None:
on_time = '9:00'
if off_time is None:
off_time = '17:00'
if off_days is None:
off_days = ['Sunday', 'Monday']
if not isinstance(on_time, datetime.time):
on_time = pd.to_datetime(on_time, format='%H:%M').time()
if not isinstance(off_time, datetime.time):
off_time = pd.to_datetime(off_time, format='%H:%M').time()
times = (index.time >= on_time) & (index.time < off_time) & (~index.weekday_name.isin(off_days))
return pd.Series(times, index=index)
|
python
|
def week_schedule(index, on_time=None, off_time=None, off_days=None):
""" Return boolean time series following given week schedule.
Parameters
----------
index : pandas.DatetimeIndex
Datetime index
on_time : str or datetime.time
Daily opening time. Default: '09:00'
off_time : str or datetime.time
Daily closing time. Default: '17:00'
off_days : list of str
List of weekdays. Default: ['Sunday', 'Monday']
Returns
-------
pandas.Series of bool
True when on, False otherwise for given datetime index
Examples
--------
>>> import pandas as pd
>>> from opengrid.library.utils import week_schedule
>>> index = pd.date_range('20170701', '20170710', freq='H')
>>> week_schedule(index)
"""
if on_time is None:
on_time = '9:00'
if off_time is None:
off_time = '17:00'
if off_days is None:
off_days = ['Sunday', 'Monday']
if not isinstance(on_time, datetime.time):
on_time = pd.to_datetime(on_time, format='%H:%M').time()
if not isinstance(off_time, datetime.time):
off_time = pd.to_datetime(off_time, format='%H:%M').time()
times = (index.time >= on_time) & (index.time < off_time) & (~index.weekday_name.isin(off_days))
return pd.Series(times, index=index)
|
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Return boolean time series following given week schedule.
Parameters
----------
index : pandas.DatetimeIndex
Datetime index
on_time : str or datetime.time
Daily opening time. Default: '09:00'
off_time : str or datetime.time
Daily closing time. Default: '17:00'
off_days : list of str
List of weekdays. Default: ['Sunday', 'Monday']
Returns
-------
pandas.Series of bool
True when on, False otherwise for given datetime index
Examples
--------
>>> import pandas as pd
>>> from opengrid.library.utils import week_schedule
>>> index = pd.date_range('20170701', '20170710', freq='H')
>>> week_schedule(index)
|
[
"Return",
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"time",
"series",
"following",
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"schedule",
"."
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/utils.py#L10-L47
|
train
|
opengridcc/opengrid
|
opengrid/library/plotting.py
|
carpet
|
def carpet(timeseries, **kwargs):
"""
Draw a carpet plot of a pandas timeseries.
The carpet plot reads like a letter. Every day one line is added to the
bottom of the figure, minute for minute moving from left (morning) to right
(evening).
The color denotes the level of consumption and is scaled logarithmically.
If vmin and vmax are not provided as inputs, the minimum and maximum of the
colorbar represent the minimum and maximum of the (resampled) timeseries.
Parameters
----------
timeseries : pandas.Series
vmin, vmax : If not None, either or both of these values determine the range
of the z axis. If None, the range is given by the minimum and/or maximum
of the (resampled) timeseries.
zlabel, title : If not None, these determine the labels of z axis and/or
title. If None, the name of the timeseries is used if defined.
cmap : matplotlib.cm instance, default coolwarm
Examples
--------
>>> import numpy as np
>>> import pandas as pd
>>> from opengrid.library import plotting
>>> plt = plotting.plot_style()
>>> index = pd.date_range('2015-1-1','2015-12-31',freq='h')
>>> ser = pd.Series(np.random.normal(size=len(index)), index=index, name='abc')
>>> im = plotting.carpet(ser)
"""
# define optional input parameters
cmap = kwargs.pop('cmap', cm.coolwarm)
norm = kwargs.pop('norm', LogNorm())
interpolation = kwargs.pop('interpolation', 'nearest')
cblabel = kwargs.pop('zlabel', timeseries.name if timeseries.name else '')
title = kwargs.pop('title', 'carpet plot: ' + timeseries.name if timeseries.name else '')
# data preparation
if timeseries.dropna().empty:
print('skipped {} - no data'.format(title))
return
ts = timeseries.resample('15min').interpolate()
vmin = max(0.1, kwargs.pop('vmin', ts[ts > 0].min()))
vmax = max(vmin, kwargs.pop('vmax', ts.quantile(.999)))
# convert to dataframe with date as index and time as columns by
# first replacing the index by a MultiIndex
mpldatetimes = date2num(ts.index.to_pydatetime())
ts.index = pd.MultiIndex.from_arrays(
[np.floor(mpldatetimes), 2 + mpldatetimes % 1]) # '2 +': matplotlib bug workaround.
# and then unstacking the second index level to columns
df = ts.unstack()
# data plotting
fig, ax = plt.subplots()
# define the extent of the axes (remark the +- 0.5 for the y axis in order to obtain aligned date ticks)
extent = [df.columns[0], df.columns[-1], df.index[-1] + 0.5, df.index[0] - 0.5]
im = plt.imshow(df, vmin=vmin, vmax=vmax, extent=extent, cmap=cmap, aspect='auto', norm=norm,
interpolation=interpolation, **kwargs)
# figure formatting
# x axis
ax.xaxis_date()
ax.xaxis.set_major_locator(HourLocator(interval=2))
ax.xaxis.set_major_formatter(DateFormatter('%H:%M'))
ax.xaxis.grid(True)
plt.xlabel('UTC Time')
# y axis
ax.yaxis_date()
dmin, dmax = ax.yaxis.get_data_interval()
number_of_days = (num2date(dmax) - num2date(dmin)).days
# AutoDateLocator is not suited in case few data is available
if abs(number_of_days) <= 35:
ax.yaxis.set_major_locator(DayLocator())
else:
ax.yaxis.set_major_locator(AutoDateLocator())
ax.yaxis.set_major_formatter(DateFormatter("%a, %d %b %Y"))
# plot colorbar
cbticks = np.logspace(np.log10(vmin), np.log10(vmax), 11, endpoint=True)
cb = plt.colorbar(format='%.0f', ticks=cbticks)
cb.set_label(cblabel)
# plot title
plt.title(title)
return im
|
python
|
def carpet(timeseries, **kwargs):
"""
Draw a carpet plot of a pandas timeseries.
The carpet plot reads like a letter. Every day one line is added to the
bottom of the figure, minute for minute moving from left (morning) to right
(evening).
The color denotes the level of consumption and is scaled logarithmically.
If vmin and vmax are not provided as inputs, the minimum and maximum of the
colorbar represent the minimum and maximum of the (resampled) timeseries.
Parameters
----------
timeseries : pandas.Series
vmin, vmax : If not None, either or both of these values determine the range
of the z axis. If None, the range is given by the minimum and/or maximum
of the (resampled) timeseries.
zlabel, title : If not None, these determine the labels of z axis and/or
title. If None, the name of the timeseries is used if defined.
cmap : matplotlib.cm instance, default coolwarm
Examples
--------
>>> import numpy as np
>>> import pandas as pd
>>> from opengrid.library import plotting
>>> plt = plotting.plot_style()
>>> index = pd.date_range('2015-1-1','2015-12-31',freq='h')
>>> ser = pd.Series(np.random.normal(size=len(index)), index=index, name='abc')
>>> im = plotting.carpet(ser)
"""
# define optional input parameters
cmap = kwargs.pop('cmap', cm.coolwarm)
norm = kwargs.pop('norm', LogNorm())
interpolation = kwargs.pop('interpolation', 'nearest')
cblabel = kwargs.pop('zlabel', timeseries.name if timeseries.name else '')
title = kwargs.pop('title', 'carpet plot: ' + timeseries.name if timeseries.name else '')
# data preparation
if timeseries.dropna().empty:
print('skipped {} - no data'.format(title))
return
ts = timeseries.resample('15min').interpolate()
vmin = max(0.1, kwargs.pop('vmin', ts[ts > 0].min()))
vmax = max(vmin, kwargs.pop('vmax', ts.quantile(.999)))
# convert to dataframe with date as index and time as columns by
# first replacing the index by a MultiIndex
mpldatetimes = date2num(ts.index.to_pydatetime())
ts.index = pd.MultiIndex.from_arrays(
[np.floor(mpldatetimes), 2 + mpldatetimes % 1]) # '2 +': matplotlib bug workaround.
# and then unstacking the second index level to columns
df = ts.unstack()
# data plotting
fig, ax = plt.subplots()
# define the extent of the axes (remark the +- 0.5 for the y axis in order to obtain aligned date ticks)
extent = [df.columns[0], df.columns[-1], df.index[-1] + 0.5, df.index[0] - 0.5]
im = plt.imshow(df, vmin=vmin, vmax=vmax, extent=extent, cmap=cmap, aspect='auto', norm=norm,
interpolation=interpolation, **kwargs)
# figure formatting
# x axis
ax.xaxis_date()
ax.xaxis.set_major_locator(HourLocator(interval=2))
ax.xaxis.set_major_formatter(DateFormatter('%H:%M'))
ax.xaxis.grid(True)
plt.xlabel('UTC Time')
# y axis
ax.yaxis_date()
dmin, dmax = ax.yaxis.get_data_interval()
number_of_days = (num2date(dmax) - num2date(dmin)).days
# AutoDateLocator is not suited in case few data is available
if abs(number_of_days) <= 35:
ax.yaxis.set_major_locator(DayLocator())
else:
ax.yaxis.set_major_locator(AutoDateLocator())
ax.yaxis.set_major_formatter(DateFormatter("%a, %d %b %Y"))
# plot colorbar
cbticks = np.logspace(np.log10(vmin), np.log10(vmax), 11, endpoint=True)
cb = plt.colorbar(format='%.0f', ticks=cbticks)
cb.set_label(cblabel)
# plot title
plt.title(title)
return im
|
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The carpet plot reads like a letter. Every day one line is added to the
bottom of the figure, minute for minute moving from left (morning) to right
(evening).
The color denotes the level of consumption and is scaled logarithmically.
If vmin and vmax are not provided as inputs, the minimum and maximum of the
colorbar represent the minimum and maximum of the (resampled) timeseries.
Parameters
----------
timeseries : pandas.Series
vmin, vmax : If not None, either or both of these values determine the range
of the z axis. If None, the range is given by the minimum and/or maximum
of the (resampled) timeseries.
zlabel, title : If not None, these determine the labels of z axis and/or
title. If None, the name of the timeseries is used if defined.
cmap : matplotlib.cm instance, default coolwarm
Examples
--------
>>> import numpy as np
>>> import pandas as pd
>>> from opengrid.library import plotting
>>> plt = plotting.plot_style()
>>> index = pd.date_range('2015-1-1','2015-12-31',freq='h')
>>> ser = pd.Series(np.random.normal(size=len(index)), index=index, name='abc')
>>> im = plotting.carpet(ser)
|
[
"Draw",
"a",
"carpet",
"plot",
"of",
"a",
"pandas",
"timeseries",
"."
] |
69b8da3c8fcea9300226c45ef0628cd6d4307651
|
https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/plotting.py#L34-L125
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
calc_pident_ignore_gaps
|
def calc_pident_ignore_gaps(a, b):
"""
calculate percent identity
"""
m = 0 # matches
mm = 0 # mismatches
for A, B in zip(list(a), list(b)):
if A == '-' or A == '.' or B == '-' or B == '.':
continue
if A == B:
m += 1
else:
mm += 1
try:
return float(float(m)/float((m + mm))) * 100
except:
return 0
|
python
|
def calc_pident_ignore_gaps(a, b):
"""
calculate percent identity
"""
m = 0 # matches
mm = 0 # mismatches
for A, B in zip(list(a), list(b)):
if A == '-' or A == '.' or B == '-' or B == '.':
continue
if A == B:
m += 1
else:
mm += 1
try:
return float(float(m)/float((m + mm))) * 100
except:
return 0
|
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calculate percent identity
|
[
"calculate",
"percent",
"identity"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L34-L50
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
remove_gaps
|
def remove_gaps(A, B):
"""
skip column if either is a gap
"""
a_seq, b_seq = [], []
for a, b in zip(list(A), list(B)):
if a == '-' or a == '.' or b == '-' or b == '.':
continue
a_seq.append(a)
b_seq.append(b)
return ''.join(a_seq), ''.join(b_seq)
|
python
|
def remove_gaps(A, B):
"""
skip column if either is a gap
"""
a_seq, b_seq = [], []
for a, b in zip(list(A), list(B)):
if a == '-' or a == '.' or b == '-' or b == '.':
continue
a_seq.append(a)
b_seq.append(b)
return ''.join(a_seq), ''.join(b_seq)
|
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skip column if either is a gap
|
[
"skip",
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"if",
"either",
"is",
"a",
"gap"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L52-L62
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
compare_seqs
|
def compare_seqs(seqs):
"""
compare pairs of sequences
"""
A, B, ignore_gaps = seqs
a, b = A[1], B[1] # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
if ignore_gaps is True:
pident = calc_pident_ignore_gaps(a, b)
else:
pident = calc_pident(a, b)
return A[0], B[0], pident
|
python
|
def compare_seqs(seqs):
"""
compare pairs of sequences
"""
A, B, ignore_gaps = seqs
a, b = A[1], B[1] # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
if ignore_gaps is True:
pident = calc_pident_ignore_gaps(a, b)
else:
pident = calc_pident(a, b)
return A[0], B[0], pident
|
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compare pairs of sequences
|
[
"compare",
"pairs",
"of",
"sequences"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L64-L77
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
compare_seqs_leven
|
def compare_seqs_leven(seqs):
"""
calculate Levenshtein ratio of sequences
"""
A, B, ignore_gaps = seqs
a, b = remove_gaps(A[1], B[1]) # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
pident = lr(a, b) * 100
return A[0], B[0], pident
|
python
|
def compare_seqs_leven(seqs):
"""
calculate Levenshtein ratio of sequences
"""
A, B, ignore_gaps = seqs
a, b = remove_gaps(A[1], B[1]) # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
pident = lr(a, b) * 100
return A[0], B[0], pident
|
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] |
calculate Levenshtein ratio of sequences
|
[
"calculate",
"Levenshtein",
"ratio",
"of",
"sequences"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L79-L89
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
pairwise_compare
|
def pairwise_compare(afa, leven, threads, print_list, ignore_gaps):
"""
make pairwise sequence comparisons between aligned sequences
"""
# load sequences into dictionary
seqs = {seq[0]: seq for seq in nr_fasta([afa], append_index = True)}
num_seqs = len(seqs)
# define all pairs
pairs = ((i[0], i[1], ignore_gaps) for i in itertools.combinations(list(seqs.values()), 2))
pool = multithread(threads)
# calc percent identity between all pairs - parallelize
if leven is True:
pident = pool.map(compare_seqs_leven, pairs)
else:
compare = pool.imap_unordered(compare_seqs, pairs)
pident = [i for i in tqdm(compare, total = (num_seqs*num_seqs)/2)]
pool.close()
pool.terminate()
pool.join()
return to_dictionary(pident, print_list)
|
python
|
def pairwise_compare(afa, leven, threads, print_list, ignore_gaps):
"""
make pairwise sequence comparisons between aligned sequences
"""
# load sequences into dictionary
seqs = {seq[0]: seq for seq in nr_fasta([afa], append_index = True)}
num_seqs = len(seqs)
# define all pairs
pairs = ((i[0], i[1], ignore_gaps) for i in itertools.combinations(list(seqs.values()), 2))
pool = multithread(threads)
# calc percent identity between all pairs - parallelize
if leven is True:
pident = pool.map(compare_seqs_leven, pairs)
else:
compare = pool.imap_unordered(compare_seqs, pairs)
pident = [i for i in tqdm(compare, total = (num_seqs*num_seqs)/2)]
pool.close()
pool.terminate()
pool.join()
return to_dictionary(pident, print_list)
|
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make pairwise sequence comparisons between aligned sequences
|
[
"make",
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"between",
"aligned",
"sequences"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L91-L110
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
print_pairwise
|
def print_pairwise(pw, median = False):
"""
print matrix of pidents to stdout
"""
names = sorted(set([i for i in pw]))
if len(names) != 0:
if '>' in names[0]:
yield ['#'] + [i.split('>')[1] for i in names if '>' in i]
else:
yield ['#'] + names
for a in names:
if '>' in a:
yield [a.split('>')[1]] + [pw[a][b] for b in names]
else:
out = []
for b in names:
if b in pw[a]:
if median is False:
out.append(max(pw[a][b]))
else:
out.append(np.median(pw[a][b]))
else:
out.append('-')
yield [a] + out
|
python
|
def print_pairwise(pw, median = False):
"""
print matrix of pidents to stdout
"""
names = sorted(set([i for i in pw]))
if len(names) != 0:
if '>' in names[0]:
yield ['#'] + [i.split('>')[1] for i in names if '>' in i]
else:
yield ['#'] + names
for a in names:
if '>' in a:
yield [a.split('>')[1]] + [pw[a][b] for b in names]
else:
out = []
for b in names:
if b in pw[a]:
if median is False:
out.append(max(pw[a][b]))
else:
out.append(np.median(pw[a][b]))
else:
out.append('-')
yield [a] + out
|
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".",
"append",
"(",
"'-'",
")",
"yield",
"[",
"a",
"]",
"+",
"out"
] |
print matrix of pidents to stdout
|
[
"print",
"matrix",
"of",
"pidents",
"to",
"stdout"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L132-L155
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
print_comps
|
def print_comps(comps):
"""
print stats for comparisons
"""
if comps == []:
print('n/a')
else:
print('# min: %s, max: %s, mean: %s' % \
(min(comps), max(comps), np.mean(comps)))
|
python
|
def print_comps(comps):
"""
print stats for comparisons
"""
if comps == []:
print('n/a')
else:
print('# min: %s, max: %s, mean: %s' % \
(min(comps), max(comps), np.mean(comps)))
|
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"(",
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")",
")",
")"
] |
print stats for comparisons
|
[
"print",
"stats",
"for",
"comparisons"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L157-L165
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
compare_clades
|
def compare_clades(pw):
"""
print min. pident within each clade and then matrix of between-clade max.
"""
names = sorted(set([i for i in pw]))
for i in range(0, 4):
wi, bt = {}, {}
for a in names:
for b in pw[a]:
if ';' not in a or ';' not in b:
continue
pident = pw[a][b]
cA, cB = a.split(';')[i], b.split(';')[i]
if i == 0 and '_' in cA and '_' in cB:
cA = cA.rsplit('_', 1)[1]
cB = cB.rsplit('_', 1)[1]
elif '>' in cA or '>' in cB:
cA = cA.split('>')[1]
cB = cB.split('>')[1]
if cA == cB:
if cA not in wi:
wi[cA] = []
wi[cA].append(pident)
else:
if cA not in bt:
bt[cA] = {}
if cB not in bt[cA]:
bt[cA][cB] = []
bt[cA][cB].append(pident)
print('\n# min. within')
for clade, pidents in list(wi.items()):
print('\t'.join(['wi:%s' % str(i), clade, str(min(pidents))]))
# print matrix of maximum between groups
comps = []
print('\n# max. between')
for comp in print_pairwise(bt):
if comp is not None:
print('\t'.join(['bt:%s' % str(i)] + [str(j) for j in comp]))
if comp[0] != '#':
comps.extend([j for j in comp[1:] if j != '-'])
print_comps(comps)
# print matrix of median between groups
comps = []
print('\n# median between')
for comp in print_pairwise(bt, median = True):
if comp is not None:
print('\t'.join(['bt:%s' % str(i)] + [str(j) for j in comp]))
if comp[0] != '#':
comps.extend([j for j in comp[1:] if j != '-'])
print_comps(comps)
|
python
|
def compare_clades(pw):
"""
print min. pident within each clade and then matrix of between-clade max.
"""
names = sorted(set([i for i in pw]))
for i in range(0, 4):
wi, bt = {}, {}
for a in names:
for b in pw[a]:
if ';' not in a or ';' not in b:
continue
pident = pw[a][b]
cA, cB = a.split(';')[i], b.split(';')[i]
if i == 0 and '_' in cA and '_' in cB:
cA = cA.rsplit('_', 1)[1]
cB = cB.rsplit('_', 1)[1]
elif '>' in cA or '>' in cB:
cA = cA.split('>')[1]
cB = cB.split('>')[1]
if cA == cB:
if cA not in wi:
wi[cA] = []
wi[cA].append(pident)
else:
if cA not in bt:
bt[cA] = {}
if cB not in bt[cA]:
bt[cA][cB] = []
bt[cA][cB].append(pident)
print('\n# min. within')
for clade, pidents in list(wi.items()):
print('\t'.join(['wi:%s' % str(i), clade, str(min(pidents))]))
# print matrix of maximum between groups
comps = []
print('\n# max. between')
for comp in print_pairwise(bt):
if comp is not None:
print('\t'.join(['bt:%s' % str(i)] + [str(j) for j in comp]))
if comp[0] != '#':
comps.extend([j for j in comp[1:] if j != '-'])
print_comps(comps)
# print matrix of median between groups
comps = []
print('\n# median between')
for comp in print_pairwise(bt, median = True):
if comp is not None:
print('\t'.join(['bt:%s' % str(i)] + [str(j) for j in comp]))
if comp[0] != '#':
comps.extend([j for j in comp[1:] if j != '-'])
print_comps(comps)
|
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print min. pident within each clade and then matrix of between-clade max.
|
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83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L167-L216
|
train
|
christophertbrown/bioscripts
|
ctbBio/compare_aligned.py
|
matrix2dictionary
|
def matrix2dictionary(matrix):
"""
convert matrix to dictionary of comparisons
"""
pw = {}
for line in matrix:
line = line.strip().split('\t')
if line[0].startswith('#'):
names = line[1:]
continue
a = line[0]
for i, pident in enumerate(line[1:]):
b = names[i]
if a not in pw:
pw[a] = {}
if b not in pw:
pw[b] = {}
if pident != '-':
pident = float(pident)
pw[a][b] = pident
pw[b][a] = pident
return pw
|
python
|
def matrix2dictionary(matrix):
"""
convert matrix to dictionary of comparisons
"""
pw = {}
for line in matrix:
line = line.strip().split('\t')
if line[0].startswith('#'):
names = line[1:]
continue
a = line[0]
for i, pident in enumerate(line[1:]):
b = names[i]
if a not in pw:
pw[a] = {}
if b not in pw:
pw[b] = {}
if pident != '-':
pident = float(pident)
pw[a][b] = pident
pw[b][a] = pident
return pw
|
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] |
convert matrix to dictionary of comparisons
|
[
"convert",
"matrix",
"to",
"dictionary",
"of",
"comparisons"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L218-L239
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/commands.py
|
setoption
|
def setoption(parser, metadata=None):
"""Set argument parser option."""
parser.add_argument('-v', action='version',
version=__version__)
subparsers = parser.add_subparsers(help='sub commands help')
create_cmd = subparsers.add_parser('create')
create_cmd.add_argument('name',
help='Specify Python package name.')
create_cmd.add_argument('-d', dest='description', action='store',
help='Short description about your package.')
create_cmd.add_argument('-a', dest='author', action='store',
required=True,
help='Python package author name.')
create_cmd.add_argument('-e', dest='email', action='store',
required=True,
help='Python package author email address.')
create_cmd.add_argument('-l', dest='license',
choices=metadata.licenses().keys(),
default='GPLv3+',
help='Specify license. (default: %(default)s)')
create_cmd.add_argument('-s', dest='status',
choices=metadata.status().keys(),
default='Alpha',
help=('Specify development status. '
'(default: %(default)s)'))
create_cmd.add_argument('--no-check', action='store_true',
help='No checking package name in PyPI.')
create_cmd.add_argument('--with-samples', action='store_true',
help='Generate package with sample code.')
group = create_cmd.add_mutually_exclusive_group(required=True)
group.add_argument('-U', dest='username', action='store',
help='Specify GitHub username.')
group.add_argument('-u', dest='url', action='store', type=valid_url,
help='Python package homepage url.')
create_cmd.add_argument('-o', dest='outdir', action='store',
default=os.path.abspath(os.path.curdir),
help='Specify output directory. (default: $PWD)')
list_cmd = subparsers.add_parser('list')
list_cmd.add_argument('-l', dest='licenses', action='store_true',
help='show license choices.')
|
python
|
def setoption(parser, metadata=None):
"""Set argument parser option."""
parser.add_argument('-v', action='version',
version=__version__)
subparsers = parser.add_subparsers(help='sub commands help')
create_cmd = subparsers.add_parser('create')
create_cmd.add_argument('name',
help='Specify Python package name.')
create_cmd.add_argument('-d', dest='description', action='store',
help='Short description about your package.')
create_cmd.add_argument('-a', dest='author', action='store',
required=True,
help='Python package author name.')
create_cmd.add_argument('-e', dest='email', action='store',
required=True,
help='Python package author email address.')
create_cmd.add_argument('-l', dest='license',
choices=metadata.licenses().keys(),
default='GPLv3+',
help='Specify license. (default: %(default)s)')
create_cmd.add_argument('-s', dest='status',
choices=metadata.status().keys(),
default='Alpha',
help=('Specify development status. '
'(default: %(default)s)'))
create_cmd.add_argument('--no-check', action='store_true',
help='No checking package name in PyPI.')
create_cmd.add_argument('--with-samples', action='store_true',
help='Generate package with sample code.')
group = create_cmd.add_mutually_exclusive_group(required=True)
group.add_argument('-U', dest='username', action='store',
help='Specify GitHub username.')
group.add_argument('-u', dest='url', action='store', type=valid_url,
help='Python package homepage url.')
create_cmd.add_argument('-o', dest='outdir', action='store',
default=os.path.abspath(os.path.curdir),
help='Specify output directory. (default: $PWD)')
list_cmd = subparsers.add_parser('list')
list_cmd.add_argument('-l', dest='licenses', action='store_true',
help='show license choices.')
|
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Set argument parser option.
|
[
"Set",
"argument",
"parser",
"option",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L12-L51
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/commands.py
|
parse_options
|
def parse_options(metadata):
"""Parse argument options."""
parser = argparse.ArgumentParser(description='%(prog)s usage:',
prog=__prog__)
setoption(parser, metadata=metadata)
return parser
|
python
|
def parse_options(metadata):
"""Parse argument options."""
parser = argparse.ArgumentParser(description='%(prog)s usage:',
prog=__prog__)
setoption(parser, metadata=metadata)
return parser
|
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] |
Parse argument options.
|
[
"Parse",
"argument",
"options",
"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L72-L77
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/commands.py
|
main
|
def main():
"""Execute main processes."""
try:
pkg_version = Update()
if pkg_version.updatable():
pkg_version.show_message()
metadata = control.retreive_metadata()
parser = parse_options(metadata)
argvs = sys.argv
if len(argvs) <= 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
control.print_licences(args, metadata)
control.check_repository_existence(args)
control.check_package_existence(args)
control.generate_package(args)
except (RuntimeError, BackendFailure, Conflict) as exc:
sys.stderr.write('{0}\n'.format(exc))
sys.exit(1)
|
python
|
def main():
"""Execute main processes."""
try:
pkg_version = Update()
if pkg_version.updatable():
pkg_version.show_message()
metadata = control.retreive_metadata()
parser = parse_options(metadata)
argvs = sys.argv
if len(argvs) <= 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
control.print_licences(args, metadata)
control.check_repository_existence(args)
control.check_package_existence(args)
control.generate_package(args)
except (RuntimeError, BackendFailure, Conflict) as exc:
sys.stderr.write('{0}\n'.format(exc))
sys.exit(1)
|
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Execute main processes.
|
[
"Execute",
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"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L80-L99
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/package.py
|
PackageData._check_or_set_default_params
|
def _check_or_set_default_params(self):
"""Check key and set default vaule when it does not exists."""
if not hasattr(self, 'date'):
self._set_param('date', datetime.utcnow().strftime('%Y-%m-%d'))
if not hasattr(self, 'version'):
self._set_param('version', self.default_version)
# pylint: disable=no-member
if not hasattr(self, 'description') or self.description is None:
getattr(self, '_set_param')('description', self.warning_message)
|
python
|
def _check_or_set_default_params(self):
"""Check key and set default vaule when it does not exists."""
if not hasattr(self, 'date'):
self._set_param('date', datetime.utcnow().strftime('%Y-%m-%d'))
if not hasattr(self, 'version'):
self._set_param('version', self.default_version)
# pylint: disable=no-member
if not hasattr(self, 'description') or self.description is None:
getattr(self, '_set_param')('description', self.warning_message)
|
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Check key and set default vaule when it does not exists.
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95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L44-L52
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/package.py
|
PackageTree.move
|
def move(self):
"""Move directory from working directory to output directory."""
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
shutil.move(self.tmpdir, os.path.join(self.outdir, self.name))
|
python
|
def move(self):
"""Move directory from working directory to output directory."""
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
shutil.move(self.tmpdir, os.path.join(self.outdir, self.name))
|
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Move directory from working directory to output directory.
|
[
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95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L169-L173
|
train
|
mkouhei/bootstrap-py
|
bootstrap_py/package.py
|
PackageTree.vcs_init
|
def vcs_init(self):
"""Initialize VCS repository."""
VCS(os.path.join(self.outdir, self.name), self.pkg_data)
|
python
|
def vcs_init(self):
"""Initialize VCS repository."""
VCS(os.path.join(self.outdir, self.name), self.pkg_data)
|
[
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Initialize VCS repository.
|
[
"Initialize",
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"."
] |
95d56ed98ef409fd9f019dc352fd1c3711533275
|
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L185-L187
|
train
|
scottrice/pysteam
|
pysteam/winutils.py
|
find_steam_location
|
def find_steam_location():
"""
Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
Steam is not installed.
"""
if registry is None:
return None
key = registry.CreateKey(registry.HKEY_CURRENT_USER,"Software\Valve\Steam")
return registry.QueryValueEx(key,"SteamPath")[0]
|
python
|
def find_steam_location():
"""
Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
Steam is not installed.
"""
if registry is None:
return None
key = registry.CreateKey(registry.HKEY_CURRENT_USER,"Software\Valve\Steam")
return registry.QueryValueEx(key,"SteamPath")[0]
|
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Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
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1eb2254b5235a053a953e596fa7602d0b110245d
|
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/winutils.py#L10-L20
|
train
|
smdabdoub/phylotoast
|
bin/PCoA_bubble.py
|
plot_PCoA
|
def plot_PCoA(cat_data, otu_name, unifrac, names, colors, xr, yr, outDir,
save_as, plot_style):
"""
Plot PCoA principal coordinates scaled by the relative abundances of
otu_name.
"""
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
for i, cat in enumerate(cat_data):
plt.scatter(cat_data[cat]["pc1"], cat_data[cat]["pc2"], cat_data[cat]["size"],
color=colors[cat], alpha=0.85, marker="o", edgecolor="black",
label=cat)
lgnd = plt.legend(loc="best", scatterpoints=3, fontsize=13)
for i in range(len(colors.keys())):
lgnd.legendHandles[i]._sizes = [80] # Change the legend marker size manually
plt.title(" ".join(otu_name.split("_")), style="italic")
plt.ylabel("PC2 (Percent Explained Variance {:.3f}%)".format(float(unifrac["varexp"][1])))
plt.xlabel("PC1 (Percent Explained Variance {:.3f}%)".format(float(unifrac["varexp"][0])))
plt.xlim(round(xr[0]*1.5, 1), round(xr[1]*1.5, 1))
plt.ylim(round(yr[0]*1.5, 1), round(yr[1]*1.5, 1))
if plot_style:
gu.ggplot2_style(ax)
fc = "0.8"
else:
fc = "none"
fig.savefig(os.path.join(outDir, "_".join(otu_name.split())) + "." + save_as,
facecolor=fc, edgecolor="none", format=save_as,
bbox_inches="tight", pad_inches=0.2)
plt.close(fig)
|
python
|
def plot_PCoA(cat_data, otu_name, unifrac, names, colors, xr, yr, outDir,
save_as, plot_style):
"""
Plot PCoA principal coordinates scaled by the relative abundances of
otu_name.
"""
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
for i, cat in enumerate(cat_data):
plt.scatter(cat_data[cat]["pc1"], cat_data[cat]["pc2"], cat_data[cat]["size"],
color=colors[cat], alpha=0.85, marker="o", edgecolor="black",
label=cat)
lgnd = plt.legend(loc="best", scatterpoints=3, fontsize=13)
for i in range(len(colors.keys())):
lgnd.legendHandles[i]._sizes = [80] # Change the legend marker size manually
plt.title(" ".join(otu_name.split("_")), style="italic")
plt.ylabel("PC2 (Percent Explained Variance {:.3f}%)".format(float(unifrac["varexp"][1])))
plt.xlabel("PC1 (Percent Explained Variance {:.3f}%)".format(float(unifrac["varexp"][0])))
plt.xlim(round(xr[0]*1.5, 1), round(xr[1]*1.5, 1))
plt.ylim(round(yr[0]*1.5, 1), round(yr[1]*1.5, 1))
if plot_style:
gu.ggplot2_style(ax)
fc = "0.8"
else:
fc = "none"
fig.savefig(os.path.join(outDir, "_".join(otu_name.split())) + "." + save_as,
facecolor=fc, edgecolor="none", format=save_as,
bbox_inches="tight", pad_inches=0.2)
plt.close(fig)
|
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Plot PCoA principal coordinates scaled by the relative abundances of
otu_name.
|
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"the",
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"abundances",
"of",
"otu_name",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/PCoA_bubble.py#L36-L65
|
train
|
smdabdoub/phylotoast
|
bin/transpose_biom.py
|
split_by_category
|
def split_by_category(biom_cols, mapping, category_id):
"""
Split up the column data in a biom table by mapping category value.
"""
columns = defaultdict(list)
for i, col in enumerate(biom_cols):
columns[mapping[col['id']][category_id]].append((i, col))
return columns
|
python
|
def split_by_category(biom_cols, mapping, category_id):
"""
Split up the column data in a biom table by mapping category value.
"""
columns = defaultdict(list)
for i, col in enumerate(biom_cols):
columns[mapping[col['id']][category_id]].append((i, col))
return columns
|
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Split up the column data in a biom table by mapping category value.
|
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"data",
"in",
"a",
"biom",
"table",
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"category",
"value",
"."
] |
0b74ef171e6a84761710548501dfac71285a58a3
|
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/transpose_biom.py#L17-L25
|
train
|
christophertbrown/bioscripts
|
ctbBio/stockholm2oneline.py
|
print_line
|
def print_line(l):
"""
print line if starts with ...
"""
print_lines = ['# STOCKHOLM', '#=GF', '#=GS', ' ']
if len(l.split()) == 0:
return True
for start in print_lines:
if l.startswith(start):
return True
return False
|
python
|
def print_line(l):
"""
print line if starts with ...
"""
print_lines = ['# STOCKHOLM', '#=GF', '#=GS', ' ']
if len(l.split()) == 0:
return True
for start in print_lines:
if l.startswith(start):
return True
return False
|
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print line if starts with ...
|
[
"print",
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"with",
"..."
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L11-L21
|
train
|
christophertbrown/bioscripts
|
ctbBio/stockholm2oneline.py
|
stock2one
|
def stock2one(stock):
"""
convert stockholm to single line format
"""
lines = {}
for line in stock:
line = line.strip()
if print_line(line) is True:
yield line
continue
if line.startswith('//'):
continue
ID, seq = line.rsplit(' ', 1)
if ID not in lines:
lines[ID] = ''
else:
# remove preceding white space
seq = seq.strip()
lines[ID] += seq
for ID, line in lines.items():
yield '\t'.join([ID, line])
yield '\n//'
|
python
|
def stock2one(stock):
"""
convert stockholm to single line format
"""
lines = {}
for line in stock:
line = line.strip()
if print_line(line) is True:
yield line
continue
if line.startswith('//'):
continue
ID, seq = line.rsplit(' ', 1)
if ID not in lines:
lines[ID] = ''
else:
# remove preceding white space
seq = seq.strip()
lines[ID] += seq
for ID, line in lines.items():
yield '\t'.join([ID, line])
yield '\n//'
|
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convert stockholm to single line format
|
[
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"to",
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"line",
"format"
] |
83b2566b3a5745437ec651cd6cafddd056846240
|
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L23-L44
|
train
|
elbow-jason/Uno-deprecated
|
uno/helpers.py
|
math_func
|
def math_func(f):
"""
Statics the methods. wut.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if len(args) > 0:
return_type = type(args[0])
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
return return_type(f(*args, **kwargs))
args = list((setify(x) for x in args))
return return_type(f(*args, **kwargs))
return wrapper
|
python
|
def math_func(f):
"""
Statics the methods. wut.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if len(args) > 0:
return_type = type(args[0])
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
return return_type(f(*args, **kwargs))
args = list((setify(x) for x in args))
return return_type(f(*args, **kwargs))
return wrapper
|
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Statics the methods. wut.
|
[
"Statics",
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"wut",
"."
] |
4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4
|
https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/helpers.py#L8-L22
|
train
|
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