--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero/libs/split_interleaved_fastq.pl	Wed Dec 06 15:59:29 2017 -0500
@@ -0,0 +1,317 @@
+#!/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 
+
+ 
\ No newline at end of file