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view FASTQ_replace_dots_for_N.py @ 0:f2939b8fb2e1 draft

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author yhoogstrate
date Thu, 19 Dec 2013 10:53:31 -0500
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children f7c90e81c05d
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#!/usr/bin/env python

import sys
from Bio import Seq, SeqRecord, SeqIO

if(sys.argv[0] == ''):
	input_stream = sys.stdin
else:
	input_stream = fh.open(sys.argv[0],"r")

for record in SeqIO.parse(input_stream,"fastq-sanger"):
	SeqIO.write(SeqRecord.SeqRecord(seq=Seq.Seq(str(record.seq).replace(".","N")),letter_annotations=record.letter_annotations,id=record.id,name=record.name,description=record.description),sys.stdout,"fastq-sanger")