Blast est-gdna sorghum.pl

#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Performs regular Blast
# -> Modyfy the infile and outfile
# Author : Rajkumar (itc@rajkumar.in)
# Release: APR 2010
# *************************************************************

# 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 $db      = "$path/sorghum/db/sgdna";
	my $query   = "$path/user/rk/pmapping/est_sorghum.fa";
	my $outfile = "$path/user/rk/pmapping/est_sorghum.blast.out";
	
	my $cpu     = "4";

# Functions
	
	print "\n\tInitiated Blast on $query .. ";
	`blastall -p blastn -d $db -i $query -e 10 -m 8 -q -5 -v 5 -o $outfile -a $cpu`;
			# -p program
			# -d database
			# -i query file
			# -e evalue
			# -m 8 tab delimited out
			# -o outfile
			# -a number of CPUs
			# -q  Penalty for a nucleotide mismatch (blastn only)   default = -3
			# -v  Number of database sequences to show one-line
			# -K  Number of best hits from a region to keep
	
	print "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