Get locus_tag list from gene list using genbank file and Biopython

Question

[spezza]

I have a list of >100 gene names and want to get the locus_tags. Is there a way I can do this using its genbank file and Biopython?

For example, the genbank file has

 /gene="murE"
 /locus_tag="BSUW23_07815"

If my list just has murE, I'd like it to print out the corresponding BSUW23_07815

[savscosta]

I'm having a similar problem

If i have a list with gene names and i want to get all the information from that gene contained in CDS and GENE in the gbk file? How could i do?

Answer 1

[Peter]

Something like this should work:

from Bio import SeqIO
​genbank_file = "example.gbk" # insert your filename here
wanted = ["murE", ...] # or load all your 100 genes from a file
for record in SeqIO.parse(genbank_file, "genbank"):
    for f in record.features:
        if f.type == "CDS" and "gene" in f.qualifiers:
            gene = f.qualifiers["gene"][0]
            if gene  in wanted:
                print f.qualifiers["gene"][0], f.qualifiers["locus_tag"][0]

See also http://www.warwick.ac.uk/go/peter_cock/python/genbank/

[spezza]

thanks! I've came across your site before and found it quite helpful... I only wish there were more examples

[savscosta]

Hello, Peter. If i have a list with gene names and i want to get all the information contained in CDS and GENE in the gbk file? How could i do?