Misa pipe.pl

#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Runs MISA : finds repeats
# -> Runs misa2p3_in.pl : Parse the repeats file and make it ready for primer3
# -> Runs Primer3
# -> Parse Primer3 results and makes a tab delimited output
# Original Author: Author: Thomas Thiel; 
# Modified by Rajkumar (itc@rajkumar.in)
# Release: JUL 2008
# *************************************************************

# Libraries
	use strict;

# At the top: Time Start
	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

# Variables
	my $path    = "/home/raj/bio";
	my $bin     = "$path/euca/ssr/bin";
	my $ssrdir  = "$path/euca/ssr/glo-gra-ssr";
	my $infile  = "$ssrdir/camal_grand.fa";
	my $program = "$path/primer3-1.1.4/src/primer3_core";
	

# Running the File
	
	chdir $bin;
	print "\tFinding Repeats..";
		`$bin/misa.pl $infile`;
	print "done.\n\tParsing Misa results..";
		`$bin/misa2p3_in.pl $infile.misa`;
	print "done.\n\tRunning Primer3 core..";
		`$program <$infile.p3in >$infile.primer`;
	print "done.\n\tParsing results..";	
		`$bin/parse_p3_results.pl $infile.primer $infile.misa`;
	print "done.\n\tAll done Man !\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