extracting data from genbank file

Question

[danka]

Hi !

I'm new in Bioinformatics, and my question may be basic to you all, but I could not find a solution on the internet....

Genom of my bacteria was sequenced and annotated a few times and I need to make a table with old and new gene names so:

The thing I want to do is to extract from all gene features locus tag and old local tag, I wrote simple lines:

from Bio import SeqIO
record = SeqIO.read('My_genome.gb', 'genbank')
for feature in record.features:
    if feature.type == 'gene':
        print ('Locus tag:', feature.qualifiers['locus_tag'])
        print ('Old Locus tag:', feature.qualifiers['old_locus_tag'])

but the problem is that sometimes, there is a new gene in My_genome and it has no old locus tag... and it stops.

What would you advise me to do, so I can obtain all of them listed?

Thank you all in advance!

Answer 1

[Andrzej Zielezinski]

You can first check if the gene has the old_locus_tag qualifier. If it doesn't, you can assign it the default value (e.g., NA). This code should do the job:

from Bio import SeqIO

record = SeqIO.read('My_genome.gb', 'genbank')

for feature in record.features: 
    if feature.type == 'gene':
        locus = feature.qualifiers.get('locus_tag', 'NA')
        locus_old = feature.qualifiers.get('old_locus_tag', 'NA')
        print('Locus tag:', locus)
        print('Old Locus tag:', locus_old)

[danka]

Thank you very much ! It works:)