Gth run

#! /usr/bin/perl -w


# *************************************************************
# This Programme does the following in sequence
# -> Runs Genome threader and outputs to a file in XML format
# Author: Rajkumar (itc@rajkumar.in)

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

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

# 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/singlet";
	my $folder  = "1";             # To be changed for each RUN
	my $resdir  = "$path/tobacco/mapping/gt/result/singlet";

	my $gth     = "$path/gt/bin/gth"; 
	my $dnadir  = "$datadir/$folder";
	my $est     = "$path/tobacco/data/est.fa";
	my $bssm    = "$path/gt/bin/bssm/arabidopsis";
	
	my ($i, $total)   = $_;
	my @files         = @_;

# Parsing the folder
	opendir (DIR, "$datadir/$folder") or die $!;
	@files = readdir(DIR);
	close(DIR);
	
	$total = @files;
	
	if (! -e "$resdir/$folder") {`mkdir $resdir/$folder`;}

	$i     = 0;
	foreach my $file(@files) {
		next if ($file eq "."  or $file eq "..");

		++$i;
		
		`$gth -genomic $dnadir/$file -cdna $est -bssm $bssm -force -xmlout -o $resdir/$folder/$file.xml`;

		my $math = $total-$i;
		print "\r\tYa. Threaded $file. Still $math to go..";
	}

	
	print "\t\nYES MAN.. All Done.\n\n";


# Running Genome Threader
	

	print "\t\nYES MAN.. All 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