<pre><code>from Bio import SeqIO
for normal, treated in zip(SeqIO.parse("/data/statistic/normal_samples", "fasta"),
                           SeqIO.parse("/data/statistic/with_treatment", "fasta")):
    ... do stuff...
</code></pre>

<p>That's generally how you <code>zip</code> iterators together in python.</p>

CC BY-SA 3.0
2018-01-31T20:42:09.413Z
2018-01-31T20:42:09.413Z
Devon Ryan
<p>My task is to count the mutations  occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (<code>SeqIO.parse</code>) in Biopython and I got all the proteins listed (separated before and after the treatment).</p>

<p>How can I zip the parsers together to count the mutations?</p>

<p>How can I count the mutations that occured after the treatment?</p>

<pre><code>from Bio import SeqIO
for normal_samples in SeqIO.parse("/data/statistic/normal_samples", "fasta"):
    print(normal_samples.id)
    print(repr(normal_samples.seq))
    print(len(normal_samples))

for treated_samples in SeqIO.parse("/data/statistic/with_treatment", "fasta"):
    print(normal_samples.id)
    print(repr(normal_samples.seq))
    print(len(normal_samples))

dict_n_t = dict(zip(normal_samples &amp; treated_samples))
</code></pre>

<python><fasta><proteins><r><mutations>
Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment
# Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

(Asked by: username_0 on 2018-01-31)

My task is to count the mutations  occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (SeqIO.parse) in Biopython and I got all the proteins listed (separated before and after the treatment).
How can I zip the parsers together to count the mutations?
How can I count the mutations that occured after the treatment?
from Bio import SeqIO
for normal_samples in SeqIO.parse("/data/statistic/normal_samples", "fasta"):
    print(normal_samples.id)
    print(repr(normal_samples.seq))
    print(len(normal_samples))

for treated_samples in SeqIO.parse("/data/statistic/with_treatment", "fasta"):
    print(normal_samples.id)
    print(repr(normal_samples.seq))
    print(len(normal_samples))

dict_n_t = dict(zip(normal_samples & treated_samples))

**Tags:** python, fasta, proteins, r, mutations

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## 1 answers

### Answer by username_1 on 2018-01-31. Score: 3 | Accepted answer

from Bio import SeqIO
for normal, treated in zip(SeqIO.parse("/data/statistic/normal_samples", "fasta"),
                           SeqIO.parse("/data/statistic/with_treatment", "fasta")):
    ... do stuff...

That's generally how you zip iterators together in python.


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