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peterjc/select_fastq2.py

Created September 7, 2011 16:29
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Selecting FASTQ sequences by ID (Biopython with strings)
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select_fastq2.py
from Bio.SeqIO.QualityIO import FastqGeneralIterator
import sys
ids = set(x[:-1] for x in open(sys.argv[1]))
for title, seq, quals in FastqGeneralIterator(sys.stdin):
if title.split(None,1)[0] in ids:
print "@%s\n%s\n+\n%s\n" % (title, seq, quals)
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