seqsero_v1: SeqSero/libs/split_interleaved

comparison SeqSero/libs/split_interleaved_fastq.pl @ 0:c577b57b7c74 draft

Uploaded

author	estrain
date	Wed, 06 Dec 2017 15:59:29 -0500
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:c577b57b7c74
+#!/usr/bin/perl-w
+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

Mercurial > repos > estrain > seqsero_v1

comparison SeqSero/libs/split_interleaved_fastq.pl @ 0:c577b57b7c74 draft