diff cf_scripts/split_for_velvet.pl @ 1:4a3afa90ff7f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cf_scripts/split_for_velvet.pl	Mon Jul 28 05:53:55 2014 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/perl
+
+use strict;
+my %read1;
+my %read2;
+my %qual1;
+my %qual2;
+
+while (my $line=<STDIN>) {
+	chomp();
+	my ($name, $flag, $chr1, $pos1, $mq, $cigar, $chr2, $pos2, $dist, $seq, $quals, $stuff)=split(/\s+/, $line);
+	if($flag & 16) {	#reverse-complement it
+		$seq=reverse($seq);
+		$seq=~tr/ACGT/TGCA/;
+		$quals=reverse($quals);
+	}
+	if($flag & 64) {	#first in pair
+		$read1{$name}=$seq;
+		$qual1{$name}=$quals;
+	}
+	else {
+		$read2{$name}=$seq;
+		$qual2{$name}=$quals;
+	}
+}
+
+open(FQ1, ">$ARGV[0]") or die "Can't open $ARGV[0]";
+open(FQ2, ">$ARGV[1]") or die "Can't open $ARGV[1]";
+open(FQ3, ">$ARGV[2]") or die "Can't open $ARGV[2]";
+
+foreach my $key(keys %read1) {
+    
+    	if(exists $read2{$key}) {
+		print FQ1 "\@$key\n$read1{$key}\n+\n$qual1{$key}\n";
+        	print FQ2 "\@$key\n$read2{$key}\n+\n$qual2{$key}\n";
+	}
+	else {
+		print FQ3 "\@$key\n$read1{$key}\n+\n$qual1{$key}\n";	
+	}
+}
+foreach my $key(keys %read2) {
+
+	if(!(exists $read1{$key})) {
+            	print FQ3 "\@$key\n$read2{$key}\n+\n$qual2{$key}\n";
+	}
+}
+close(FQ1);
+close(FQ2);
+close(FQ3);
+
+
+
+ 
\ No newline at end of file