Tgicl parse.pl

#! /usr/bin/perl -w


# *************************************************************
# This Programme does the following in sequence
# -> Open a results folder of TGICL
# -> parse the contigs and singlets
# -> Output as multifasta of single file
# Author: Rajkumar (itc@rajkumar.in)

# *************************************************************

# Libraries
	use strict;
	use Bio::SeqIO;
	use Bio::Perl;

## Variables
	my $path     = "/home/raj/bio";
	my $resdir   = "$path/euca/unigene";

	my $singlets = "$resdir/globulus_singlets.fa";
	my $contigs  = "$resdir/globulus_contigs.fa";
	my $unigenes = "$resdir/globulus_unigenes.fa";
	

	my @asmdir   = ("asm_1", "asm_2", "asm_3", "asm_4");

# Getting the grip
	if (-e "$singlets") {`rm  $singlets`;}
	if (-e "$contigs") {`rm  $contigs`;}
	if (-e "$unigenes") {`rm  $unigenes`;}
		
	foreach my $asm (@asmdir) {
		`cat $resdir/result/$asm/contigs >>$contigs`;	
		`cat $resdir/result/$asm/singlets >>$singlets`;
	}
	`cat $contigs $singlets >$unigenes`;
	

# END