Raj at 08:38, 20 May 2016

2016-05-20T08:38:12Z

← Older revision		Revision as of 08:38, 20 May 2016
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	</source>		</source>
			[[Category:Bioinformatics]]

Raj at 06:04, 2 January 2010

2010-01-02T06:04:14Z

← Older revision		Revision as of 06:04, 2 January 2010
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	<~~pre~~>		<source lang=perl>
	#! /usr/bin/perl -w		#! /usr/bin/perl -w

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	# END		# END

	</~~pre~~>		</source>

Raj: New page:

 #! /usr/bin/perl -w   # ************************************************************* # This Programme does the following in sequence # -> Runs Genome threader and outputs to a file ...

2009-11-01T17:15:07Z

New page: <pre> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Runs Genome threader and outputs to a file ...

New page

<pre>
#! /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

</pre>

Gth run - Revision history

Raj at 08:38, 20 May 2016

Raj at 06:04, 2 January 2010

Raj: New page:
#! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Runs Genome threader and outputs to a file ...