/usr/share/seqsero/libs/split_interleaved_fastq.pl is in seqsero 1.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use File::Basename;
# Date: 14-05-2010
# This program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order.
# Author: Ram Vinay Pandey
# Define the variables
my $input="";
my $output="";
my $help=0;
my $test=0;
my $verbose=1;
my $usage="perl $0 --input interleaved_fastq_file.fastq --output output.fastq\n";
GetOptions(
"input=s" =>\$input,
"output=s" =>\$output,
"test" =>\$test,
"help" =>\$help
) or pod2usage(-msg=>"Wrong options",-verbose=>1);
pod2usage(-verbose=>2) if $help;
Test::runTests() if $test;
pod2usage(-msg=>"\n\tProvide an input file!!\n\n\t\t$usage\n\n",-verbose=>1) unless -e $input;
pod2usage(-msg=>"\n\tProvide an output file!!\n\n\t\t$usage\n\n",-verbose=>1) unless $output;
my ( $name, $path, $extension ) = File::Basename::fileparse ( $output, '\..*' );
my $output1 = $name."-read1.fastq";
my $output2 = $name."-read2.fastq";
open my $ofh1, ">$output1" or die "Could not open output file";
open my $ofh2, ">$output2" or die "Could not open output file";
open (IN, "<$input") or die ("Could not open file $input for reading\n");
while (<IN>) {
chomp;
s/\r/\n/g;
# discard blank line
if (m/^\s*$/g) {
next;
}
else {
# Reading all lines for read 1
if (m/^\s*\@.*1$/) {
print $ofh1 "$_\n";
my $ct=0;
while(my $l = <IN>) {
$ct++;
chomp $l;
s/\r/\n/g;
print $ofh1 "$l\n";
last if($ct ==3);
}
}
# Reading all lines for read 2
if (m/^\s*\@.*2$/) {
print $ofh2 "$_\n";
my $ct=0;
while(my $l = <IN>) {
$ct++;
chomp $l;
s/\r/\n/g;
print $ofh2 "$l\n";
last if($ct ==3);
}
}
}
}
close IN;
close $ofh1;
close $ofh2;
=head1 NAME
split-interleaved-fastq.pl - TThis program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order.
=head1 SYNOPSIS
perl split-interleaved-fastq.pl --input interleaved_fastq_file.fastq --output output.fastq
=head1 OPTIONS
=over 4
=item B<--input>
The input file which contains read1 and read2 in a single file in FASTQ format. Mandatory parameter
=item B<--output>
The output file. Mandatory parameter
=item B<--help>
Display help for this script
=back
=head1 Details
=head2 Input
The paired-end reads in interleaved format; input file looks like following:
@fc_HWUSI-EAS613R:1:1:4:682#CATA/1
TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG
+fc_HWUSI-EAS613R:1:1:4:682#CATA/1
baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV
@fc_HWUSI-EAS613R:1:1:4:682#CATA/2
TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA
+fc_HWUSI-EAS613R:1:1:4:682#CATA/2
bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
=head2 Output
The output looks like as following for reads 1:
@fc_HWUSI-EAS613R:1:1:4:682#CATA/1
TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG
+fc_HWUSI-EAS613R:1:1:4:682#CATA/1
baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV
The output looks like as following for reads 2:
@fc_HWUSI-EAS613R:1:1:4:682#CATA/2
TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA
+fc_HWUSI-EAS613R:1:1:4:682#CATA/2
bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
=head1 AUTHORS
Ram vinay pandey
=cut
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