# HG changeset patch
# User jampradinuk
# Date 1336684757 14400
# Node ID f87183778470722efc898dfb5b015fcdd316f565
# Parent  a8eccdcc080009338fce8e4c7d4ac797660ce257
Uploaded

diff -r a8eccdcc0800 -r f87183778470 fastq_paired_reads_convention.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_paired_reads_convention.pl	Thu May 10 17:19:17 2012 -0400
@@ -0,0 +1,50 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+
+# fastq_paired_reads_convention2.pl [input file] [left output file] [right output file]
+
+die "Check arguments" unless @ARGV == 3;
+
+#open (LEFT, '>data/left2.fastq') or die "Cannot create $ARGV[1]: $!\n";
+#open (RIGHT, '>data/right2.fastq') or die "Cannot create $ARGV[2]: $!\n";
+#open (INPUT, '<data/interlaced.fastq') or die "Cannot open $ARGV[0]: $!\n";
+
+open (LEFT, '>', $ARGV[1]) or die "Cannot create $ARGV[1]: $!\n";
+open (RIGHT, '>', $ARGV[2]) or die "Cannot create $ARGV[2]: $!\n";
+open (INPUT, '<', $ARGV[0]) or die "Cannot open $ARGV[0]: $!\n";
+
+my $which = 0;
+my $current_id;
+
+while(<INPUT>) {
+	chomp;
+	if(/ 1\S*/){
+		$_ =~ s/ 1\S*//;
+		$_.='/1';
+		$current_id = substr $_, 1;
+		$which = 1;
+	}
+	if(/ 2\S*/){
+		$_ =~ s/ 2\S*//;
+		$_.='/2';
+		$current_id = substr $_, 1;
+		$which = 2;
+	}
+	
+	if($_ eq '+'){
+		$_.=$current_id;
+	}
+	
+	if($which == 1){
+		print LEFT "$_\n";
+	}
+	if($which == 2){
+		print RIGHT "$_\n";
+	}
+}
+
+close (LEFT);
+close (RIGHT);
+close (INPUT);
\ No newline at end of file