<p>Your answer looks like a good start. You'll probably want to use sys.argv, argparse, or another argument parsing tool to read in options from the command line, then compare them to the fields (e.g. the &quot;type&quot; argument gets compared with the type column).</p>
<p>Given that attributes can be arranged in an arbitrary order, you'll probably need to read all of them from each line and store in a dict in order to determine whether the target is present. A regular expression search is another way to do that.</p>
<p>There are a few libraries available (e.g. from biopython) for reading and subsetting FASTA records.</p>

CC BY-SA 4.0
2021-04-22T05:37:11.940Z
2021-04-22T05:37:11.940Z
gringer
<p>Problem Statement</p>
<blockquote>
<p>The GFF3 format is a commonly-used one in bioinformatics for
representing sequence  annotation. You can find the specification
here:</p>
<p><a href="http://www.sequenceontology.org/gff3.shtml" rel="nofollow noreferrer">http://www.sequenceontology.org/gff3.shtml</a></p>
<p>The genome and annotation for Saccharomyces cerevisiae S288C is on the
class server here:</p>
<pre><code>/home/jorvis1/Saccharomyces_cerevisiae_S288C.annotation.gff
</code></pre>
<p>Note that this same file has both the annotation feature table and the
FASTA sequence for the  molecules referenced. (See the '##FASTA'
directive in the specification.) Within the feature table another
column of note is the 9 th , where we can store any key=value  pairs
relevant to that row's feature such as ID, Ontology_term or Note. Your
task is to write a GFF3 feature exporter. A user should be able to run
your script like this:</p>
<pre><code>$ export_gff3_feature.py --source_gff=/path/to/some.gff3 --type=gene --attribute=ID --value=YAR003W
</code></pre>
<p>There are 4 arguments here that correspond to values in the GFF3
columns. In this case, your  script should read the path to a GFF3
file, find any gene (column 3) which has an ID=YAR003W (column 9).
When it finds this, it should use the coordinates for that feature
(columns 4, 5 and 7)  and the FASTA sequence at the end of the
document to return its FASTA sequence. Your script should work
regardless of the parameter values passed, warning the user if no
features were found that matched their query. (It should also check
and warn if more than one  feature matches the query.)</p>
<p>The output should just be printed on STDOUT (no writing to a file is
necessary.) It should have a header which matches their query, like
this:</p>
<blockquote>
<p>gene:ID:YAR003W .... sequence here ...</p>
</blockquote>
<p>As an extra challenge, you can format the sequence portion of the
FASTA output as 60-characters per line, which follows the standard.</p>
</blockquote>
<p>So far I have this below. I'm not even sure if this is correct to start with:</p>
<pre><code>#!/usr/bin/env python3

for line in open(&quot;Saccharomyces_cerevisiae_S288C.annotation.gff&quot;):
   line1 = line.rstrip()
   if line.startswith(&quot;#&quot;):
       continue
   column = line1.split(&quot;\t&quot;)
   if len(column) != 9:
       continue
   id = column[8]
   type = column[2]
</code></pre>
<p>Can anyone help me with this? I'm totally lost. Thank you!</p>

CC BY-SA 4.0
2022-10-22T11:19:26.750Z
Was there any restriction about using already developed packages for this purpose? If not : https://biopython.org/wiki/GFF_Parsing , you can wrap your script around with this plus argparse to work from the console: https://docs.python.org/3/library/argparse.html
Avamys
CC BY-SA 4.0
2022-10-22T21:50:10.770Z
@Avamys please add this as a separate answer. Comments should only be used for transient information that can help improve or supplement questions or answers. See [here](https://bioinformatics.stackexchange.com/help/privileges/comment) for more information.
gringer
<gff3><homework>
Create GFF3 feature exporter
# Create GFF3 feature exporter

(Asked by: username_0 on 2021-04-21)

Problem Statement

The GFF3 format is a commonly-used one in bioinformatics for
representing sequence  annotation. You can find the specification
here:
http://www.sequenceontology.org/gff3.shtml
The genome and annotation for Saccharomyces cerevisiae S288C is on the
class server here:
/home/jorvis1/Saccharomyces_cerevisiae_S288C.annotation.gff

Note that this same file has both the annotation feature table and the
FASTA sequence for the  molecules referenced. (See the '##FASTA'
directive in the specification.) Within the feature table another
column of note is the 9 th , where we can store any key=value  pairs
relevant to that row's feature such as ID, Ontology_term or Note. Your
task is to write a GFF3 feature exporter. A user should be able to run
your script like this:
$ export_gff3_feature.py --source_gff=/path/to/some.gff3 --type=gene --attribute=ID --value=YAR003W

There are 4 arguments here that correspond to values in the GFF3
columns. In this case, your  script should read the path to a GFF3
file, find any gene (column 3) which has an ID=YAR003W (column 9).
When it finds this, it should use the coordinates for that feature
(columns 4, 5 and 7)  and the FASTA sequence at the end of the
document to return its FASTA sequence. Your script should work
regardless of the parameter values passed, warning the user if no
features were found that matched their query. (It should also check
and warn if more than one  feature matches the query.)
The output should just be printed on STDOUT (no writing to a file is
necessary.) It should have a header which matches their query, like
this:

gene:ID:YAR003W .... sequence here ...

As an extra challenge, you can format the sequence portion of the
FASTA output as 60-characters per line, which follows the standard.

So far I have this below. I'm not even sure if this is correct to start with:
#!/usr/bin/env python3

for line in open("Saccharomyces_cerevisiae_S288C.annotation.gff"):
   line1 = line.rstrip()
   if line.startswith("#"):
       continue
   column = line1.split("\t")
   if len(column) != 9:
       continue
   id = column[8]
   type = column[2]

Can anyone help me with this? I'm totally lost. Thank you!

**Tags:** gff3, homework
> **Comments:**
> **username_1**: Was there any restriction about using already developed packages for this purpose? If not : https://biopython.org/wiki/GFF_Parsing , you can wrap your script around with this plus argparse to work from the console: https://docs.python.org/3/library/argparse.html  
> **username_2**: @Avamys please add this as a separate answer. Comments should only be used for transient information that can help improve or supplement questions or answers. See [here](https://bioinformatics.stackexchange.com/help/privileges/comment) for more information.  

---

## 1 answers

### Answer by username_2 on 2021-04-22. Score: 0

Your answer looks like a good start. You'll probably want to use sys.argv, argparse, or another argument parsing tool to read in options from the command line, then compare them to the fields (e.g. the "type" argument gets compared with the type column).

Given that attributes can be arranged in an arbitrary order, you'll probably need to read all of them from each line and store in a dict in order to determine whether the target is present. A regular expression search is another way to do that.

There are a few libraries available (e.g. from biopython) for reading and subsetting FASTA records.


---

