--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shuffleSequences_fasta.pl	Tue Jun 07 17:42:21 2011 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/perl
+
+if (!@ARGV) {
+	print "Usage: $0 forward_reads.fa reverse_reaads.fa outfile.fa\n";
+	print "\tforward_reads.fa / reverse_reads.fa : paired reads to be merged\n";
+	print "\toutfile.fa : outfile to be created\n";
+	system.exit(0);	
+}
+
+$filenameA = $ARGV[0];
+$filenameB = $ARGV[1];
+$filenameOut = $ARGV[2];
+
+die "Could not open $filenameA" unless (-e $filenameA);
+die "Could not open $filenameB" unless (-e $filenameB);
+
+open FILEA, "< $filenameA";
+open FILEB, "< $filenameB";
+
+open OUTFILE, "> $filenameOut";
+
+my ($lineA, $lineB);
+
+$lineA = <FILEA>;
+$lineB = <FILEB>;
+
+while(defined $lineA) {
+	print OUTFILE $lineA;
+	$lineA = <FILEA>;
+	while (defined $lineA && $lineA !~ m/>/) { 
+		print OUTFILE $lineA;
+		$lineA = <FILEA>;
+	}
+
+	print OUTFILE $lineB;
+	$lineB = <FILEB>;
+	while (defined $lineB && $lineB !~ m/>/) { 
+		print OUTFILE $lineB;
+		$lineB = <FILEB>;
+	}
+}