Bulk sequence renaming with BioPython

bulk_sequence_rename.py

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')

Nice, thanks for this ! (It worked perfectly right away)