Assemble ITC EST-TOBEA EST

#! /usr/bin/perl -w
 
# *************************************************************
# This Programme does the following in sequence
# -> Assembles ITC and TOEA ESTs
# -> Multicored
# Author : Rajkumar (itc@rajkumar.in)
# Release: APR 2010
# *************************************************************
 
# Libraries
	use strict;
	use Bio::Perl;
	use Bio::SearchIO;
	use Parallel::ForkManager;

 
# At the top: Time Start
	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
 
# Variables
	my $path     = "/home/raj/bio";
	my $datadir  = "$path/tobacco/data";
	my $est      = "$datadir/est.fa";
	my $resdir  = "$datadir/unigene_result";
	
	my $pm = new Parallel::ForkManager(16);
	 
	my $tgicl   = "$path/tgicl/tgicl";
	my $cpu     = "16";
 
	my ($i)    = $_;
	my (@files)= @_;
 

# Clear the Files
	
	if (-e "$resdir") {`rm -fr $resdir`;}
	if (! -e "$resdir") {`mkdir $resdir`;}


 
# Parsing the Contigs
	chdir "$path/tgicl";
	`$tgicl $est -c $cpu -l 40 -p 94 -M`;
			# -l miminum overlap length (default 40)
			# -M ignore lower-case masking in <fasta_db> sequences
			# -p minimum percent identity for overlaps <PID> (default 94)

	print "\n\tAll Done!\n\n";
	
 
# At the End: Time Calculation
	my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);
	my $days  = $mday_-$mday;
	my $hours = $hour_-$hour;
	my $mins  = $min_-$min;
	my $secs  = $sec_-$sec;
	print "\n------------------------\nDuration: ";
	if ($days>0) { print "$days days";}
	if ($hours>0) { print ": $hours hours";}
	if ($mins>0) { print ": $mins mins";}
	if ($secs>0) { print ": $secs secs";}
	print "\n------------------------\n";
 
# END