Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Runs TGICL Program to assemble ...

2009-12-26T15:13:14Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Runs TGICL Program to assemble ...

New page

<source lang=perl>
#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Runs TGICL Program to assemble ESTs
# -> Contigs and Single
# 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 $est = "$path/euca/ssr/data/globulus_est_repeat.fa";
my $resdir = "$path/euca/unigene/result";

my $tgicl = "$path/tgicl/tgicl";
my $cpu = "4";

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

chdir $resdir;

`$tgicl $est -c $cpu -l 35 -p 90 -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 "\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

</source>

Tgcl run.pl - Revision history

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Runs TGICL Program to assemble ...