Raj at 13:24, 28 April 2010

2010-04-28T13:24:17Z

← Older revision		Revision as of 13:24, 28 April 2010
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	# END		# END

	</~~perl~~>		</source>

	[[Category: Bioinformatics]]		[[Category: Bioinformatics]]

Raj: Created page with ' #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Reads the 2 files (T…'

2010-04-28T13:23:49Z

Created page with '<source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Reads the 2 files (T…'

New page

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

# *************************************************************
# This Programme does the following in sequence
# -> Reads the 2 files (TGI)
# -> Reads the fasta, name appropriately and writes a concatenated outfile
# Author : Rajkumar (itc@rajkumar.in)
# Release: APR 2010
# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SearchIO;
use Parallel::ForkManager;

# 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";
my $singlet = "$datadir/tgi_singlet.fa";
my $contig = "$datadir/tgi_contig.fa";
my $outfile = "$datadir/tgi.fa";

my $pm = new Parallel::ForkManager(16);

my ($i) = $_;
my (@files)= @_;

# Clear the Files

if (-e "$outfile") {`rm $outfile`;}

# Parsing the Contigs
print "\n\tParsing Contigs..";

my $in = Bio::SeqIO->new(-file => "$contig", -format => 'Fasta');
my $identifier;
my $sequence;

while ( my $seq = $in->next_seq() ) {

$pm->start and next;

$identifier = $seq->id;
$sequence = $seq->seq;

$identifier = "TGI_CON_".$identifier;

my ($fasta) = $_;
$fasta = ">$identifier\n$sequence\n";

open (F, ">>".$outfile);
print F $fasta;
close F;

$pm->finish;
}

$pm->wait_all_children;
print " Done!\n";

# Parsing the Singlet

print "\n\tParsing Singlets..";

$in = Bio::SeqIO->new(-file => "$singlet", -format => 'Fasta');

while ( my $seq = $in->next_seq() ) {

$pm->start and next;

$identifier = $seq->id;
$sequence = $seq->seq;

$identifier = "TGI_SIG_".$identifier;

my ($fasta) = $_;
$fasta = ">$identifier\n$sequence\n";

open (F, ">>".$outfile);
print F $fasta;
close F;

$pm->finish;
}

$pm->wait_all_children;
print " Done!\n";

print "\n\tAll 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

</perl>

[[Category: Bioinformatics]]

Rename TGI - Revision history

Raj at 13:24, 28 April 2010

Raj: Created page with ' #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Reads the 2 files (T…'