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I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions. Here is one accession and here is a link to its COX1 gene, which I found manually on that page.

I have downloaded all the accessions as an XML genbank file:

#!/usr/bin/env python3

from Bio import Entrez
from Bio import GenBank
from Bio import SeqIO
import os


if os.path.exists('cats.xml') ==False:
    with open('accessions.txt', 'r') as fin:
        #for line
        accs = [line.rstrip() for line in fin ]

    print(accs)

    Entrez.email =  "[email protected]"
    rec = Entrez.efetch(db='nuccore', id=accs, rettype="gb", retmode="xml")
    with open('cats.xml', 'w') as out:
        print(rec.read().decode("utf-8"), file=out)

Then I tried to parse this file:

with open('cats.xml', 'rb') as xin:
    for record  in Entrez.parse(xin):
        #print(dir(record))
        #print(record.keys())
        pass
print(record['GBSeq_feature-table'][0])

But it's a mess of nested lists and dictionaries. Help!

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  • $\begingroup$ Please edit your question and show us the output you expect from your example input. I get what looks like a perfectly normal and valid JSON output. What exactly do you need? COX1 gene accessions? DNA sequence? cDNA sequence? Protein translation? $\endgroup$
    – terdon ♦
    Nov 20, 2021 at 11:48

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