RepeatAnalysisFastqToSplitFasta.py

#! /usr/bin/env python

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## Author: Brett Bowman

import sys

from pbcore.io import FastqReader, FastaRecord, FastaWriter

outputPrefix = sys.argv[1]
fns = sys.argv[2:]

seqIds = set()
for fn in fns:
    for record in FastqReader(fn):
        if record.id in seqIds:
            print "ERROR: Duplicate sequence id '{0}'".format(record.id)
            raise SystemExit
        with FastaWriter( outputPrefix + "." + record.id + ".fasta" ) as handle:
            fasta = FastaRecord(record.id, record.sequence)
            handle.writeRecord( fasta )
        seqIds.add( record.id )