/
fastq_split.pl
executable file
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/
fastq_split.pl
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#!/usr/bin/perl -w
use strict;
use Getopt::Long;
use File::Spec;
my %uncompress = (
'bz2' => 'bzcat',
'gz' => 'zcat'
);
# assume short read fastq with 4 lines per record!
my $size = 1_000_000;
my $outdir;
if ( !defined @ARGV ) {
print "Please Provide
-s int The number of sequences per file [1_000_000]
-o dir The name of the directory to output the files
followed by a list of files to be split
Usage:
./fastq_split -o split_fq ~/somedir/someRandom.fq
./fastq_split -s 1000 -o split_fq ~/somedir/*fq
";
exit;
}
GetOptions(
's|size:i' => \$size,
'o|outdir:s' => \$outdir,
);
my @files = @ARGV;
if ( !-e $outdir ) {
system("mkdir -p $outdir");
}
for my $file (@files) {
$file = File::Spec->rel2abs($file);
my ( $vol, $dir, $fname ) = File::Spec->splitpath($file);
my $odir = $outdir || $dir;
my $fh;
if ( $fname =~ /(\S+)\.(gz|bz2)$/ ) {
open( $fh => "$uncompress{$2} $file |" ) || die $!;
$fname = $1;
}
else {
open( $fh => $file ) || die "$file $!";
}
my @name = split( /\./, $fname );
my ($ext) = pop @name;
my $f = join( ".", @name );
my $i = 0;
open( my $ofh => sprintf( ">$odir/p%02d.%s.%s", $i++, $f, $ext ) ) || die $!;
my $n = 0;
while (<$fh>) {
unless (/^@/) {
chomp;
die(
"out of register, got line:\n$_\n but expected line to start with '\@'\n"
);
}
print $ofh $_;
for ( 0 .. 2 ) {
$_ = <$fh>;
print $ofh $_;
}
if ( ++$n >= $size ) {
close($ofh);
open( $ofh => sprintf( ">$odir/p%02d.%s.%s", $i++, $f, $ext ) ) || die $!;
$n = 0;
}
}
close($ofh);
}