Hello everyone.. I am quite new in here also with biopython.
I have a set of protein ids, using them i extracted locus_tags from genbank file, But i wonder if there is a way to extract locations of those genes i.e. start and end position using existing information??
for example: I have two files,
- genbank file
- text file containing protein_ids
using this protein id file, i need to get start and end positions of the corresponding gene from that gbk file.
Many thanks and i really appreciate this service.. :)
1 answer
You should be able to make a script that will reference the protein file and the genbank file and either append the protein file or just make a new one. For the looping through of the genbank file you can use this loop from one of my scripts
for record in SeqIO.parse(open(gb_file,"rU"),"genbank"):
for feature in record.features:
if feature.type == 'CDS':
start = int(feature.location.start)
stop = int(feature.location.end)
try:
name = feature.qualifiers['gene'][0]
except:
#some features only have locus tags
name = feature.qualifiers['locus_tag'][0]
if feature.strand < 0:
strand = "-"
else:
strand = "+"
bed_line = record.id +"\t{0}\t{1}\t{2}\t500\t{3}\t{0}\t{1}\t50,205,50\n".format(start, stop, name,strand)
out_bedfile.write(bed_line)
this should get you wan you want, you can find the whole script here More file parsing :) EDIT how do I make a fast and bed file from Genbank file - SOLVED
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Could be helpful : How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
BiomaRt : http://www.ensembl.info/blog/2015/06/01/biomart-or-how-to-access-the-ensembl-data-from-r/
But i am looking for the gene location on genome, as we know in genbank file, for each gene start and end co-rodinates are given, using existing information i.e. gene i.d or locus tag, i would like to get those start and end co-ordinates of corresponding genes.
Please add an example .