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#!/usr/bin/perl
#------------------------------------------------------------------------------
# Split a fastq file into N sequences per file
#
# WARNING: It assumes FASTQ sequences are in four-line
# format. I.e. no multi-line sequences or qualities
#
# Pablo Cingolani
#------------------------------------------------------------------------------
use strict;
die "Usage: fastqSplit.pl numSequences file.fastq prefix\n" if $#ARGV != 2;
my($numSeqs) = $ARGV[0]; # Number of sequences per file
my($fastq) = $ARGV[1]; # Original files name
my($outPrefix) = $ARGV[2]; # Output file names prefix
#------------------------------------------------------------------------------
# Main
#------------------------------------------------------------------------------
# Open file
if( $fastq =~ /\.gz$/ ) { open FQ, "gunzip -c $fastq |" or die "Cannot open input file '$fastq'\n"; }
else { open FQ, "$fastq" or die "Cannot open input file '$fastq'\n"; }
# Read sequences
my($seqName, $seq, $seqName2, $qual, $outFq, $l);
my($lineNum, $outSeqNum, $seqNum, $fileNum) = (1, 1, 1, 1);
for($seqNum=1 ; $seqName = <FQ> ; $seqNum++ ) {
$seq = <FQ>;
$seqName2 = <FQ>;
$qual = <FQ>;
# Sanity check
die "Error parsing sequence number $seqNum (line $lineNum): Sequence name does not start with '\@'\n" if( $seqName !~ /^\@/ );
die "Error parsing sequence number $seqNum (line $lineNum): Sequence quality name does not start with '+'\n" if( $seqName2 !~ /^\+/ );
# Open a new output file?
if(($outFq eq '') || ($outSeqNum > $numSeqs)) {
# Create a files name using 'prefix'
$outFq = sprintf( "%s.%03d.fastq", $outPrefix, $fileNum);
print "$outFq\n";
$fileNum++;
$outSeqNum = 1;
# Open new file (close old one)
close OUT if $outFq ne '';
open OUT,"> $outFq" or die "Cannot open output file '$outFq'\n";
}
# Output to file
print OUT "$seqName$seq$seqName2$qual";
$lineNum += 4;
$outSeqNum++;
$seqNum++;
}
close FQ;
close OUT;
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