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peterjc/select_fastq.py

Created September 7, 2011 16:27
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Selecting FASTQ sequences by ID (Biopython with SeqRecord object)
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select_fastq.py
from Bio import SeqIO
import sys
ids = set(x[:-1] for x in open(sys.argv[1]))
wanted = (rec for rec in SeqIO.parse(sys.stdin, "fastq") if rec.id in ids)
SeqIO.write(wanted, sys.stdout, "fastq")
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