bulk sequence renaming with biopython

31 Aug 2010 \\ bioinformatics  python 

Sometimes large, genome-size files are not named like you want them to be. Most of them are large and it's easier to rename them programmatically. Here is one way to do that, using BioPython.

from Bio import SeqIO

# create a dict to hold our new GI:names mapping, which looks like so, in 
# this case (from sheep)
#
# gi|289623201|gb|CM000885.1|   299839927   chr1
# gi|289623190|gb|CM000894.1|   94216033     chr10
# gi|289623189|gb|CM000895.1|   67137890     chr11
# gi|289623188|gb|CM000896.1|   86457535     chr12
data = {}

# read in this file, split it into a dict
for line in open('oviAri1 copy.info','rU').readlines():
    line_split = line.strip('\n').split('\t')
    data[line_split[0]] = line_split[2]

# open a file for the output
output_file = open('new_oviAri1_seq.fa','w')

# create an iterable to hold the new data
new_seq = []

# iterate over seq, updating the name.  This is going to give us something like:
#
# >chr1
# 
for record in SeqIO.parse(open('oviAri1.fa','rU'),'fasta'):
    new_record_name = data[record.id]
    record.id = new_record_name
    record.name = ''
    record.description = ''
    new_seq.append(record)

# write the whole thing out
SeqIO.write(new_seq, output_file, 'fasta')

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