Hi - I am using biopython (open to any other method however) to find sequences in a fasta file that match ID's from a .txt file. Just by looking at the two files I can see there are matches, but the following script will not find them:

#!/usr/bin/env python

import sys
from Bio import SeqIO

input_file = sys.argv[1]
id_file = sys.argv[2]
output_file = sys.argv[3]

wanted = set(line.rstrip("\n").split(None,1)[0] for line in open(id_file))
print "Found %i unique identifiers in %s" % (len(wanted), id_file)

records = (r for r in SeqIO.parse(input_file, "fasta") if r.id in wanted)
count = SeqIO.write(records, output_file, "fasta")

print "Saved %i records from %s to %s" % (count, input_file, output_file)
if count < len(wanted):
    print "Warning %i IDs not found in %s" % (len(wanted)-count, input_file)

here is a snippet of the fasta file (.fasta):

>gnl|TC-DB|P0A334 1.A.1.1.1 Voltage-gated potassium channel OS=Streptomyces lividans GN=kcsA PE=1 SV=1
MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLI
TYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQE
RRGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR
>gnl|TC-DB|P06550 1.A.1.1.2 LctB protein - Bacillus stearothermophilus.
MDYAFLGVVTAVLLGSITSLWTASVQATHRLSLDSLWVLVQWYGTMLLGFAMIYMILQAN
GHHVFTPSPSSAAGNRLSMLEDSLYLSGMTLLSVGYGDVTPVGIGRWIAIAEALLGYIMP
AVIVTRTVFDSDRR

and the id file (.txt)

Q09666 
Q7PMK5 
P98161 
A0CX44 
Q23K98 
P29993 
Q9VLS3 
Q14643 
Q9H5I5 
Q4E330 
P29995

I don't think there is a problem with the python script, but maybe the fasta file. can anyone spot anything strange. I know for a fact all id's match.

Thanks very much,

Arron.