Raj: Created page with 'Category:Bioinformatics * Assembling ~50000 ESTs Took 3.5 hours under 8 core both run and parse scripts are below #! /usr/bin/perl -w # *********…'

2010-09-19T19:07:10Z

Created page with 'Category:Bioinformatics * Assembling ~50000 ESTs ** Took 3.5 hours under 8 core ** both run and parse scripts are below <source lang=perl> #! /usr/bin/perl -w # *********…'

New page

[[Category:Bioinformatics]]

* Assembling ~50000 ESTs
** Took 3.5 hours under 8 core
** both run and parse scripts are below

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

# *************************************************************
# This Programme does the following in sequence
# -> Makes a single fasta
# -> Runs TGICL Program to assemble Ret files
# -> Contigs and Single
# Author: Rajkumar (r@rajkumar.in)
# Release: SEP 2010

# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SeqIO;
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 $curdir = "$path/user/rk/castor/unigene";
my $resdir = "$curdir/result";
my $data = "$curdir/data/castorEST.txt";

my $tgicl = "$path/tgicl/tgicl";
my $cpu = "8";

my ($i, $total, $file) = $_;
my @files = @_;

#Multi-threading
my $midstop = "0";
my $pm = new Parallel::ForkManager(1);

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

# Getiing into the folder

my $in = Bio::SeqIO->new(-file => "$data", -format => 'Fasta');
my ($identifier, $sequence) = $_;
while ( my $seq = $in->next_seq() ) {
$identifier = $seq->id;
$sequence = $seq->seq;
$identifier =~ s/\|/_/g;

my $fasta = ">".$identifier."\n".$sequence."\n";

open (F, ">>".$resdir."/castorEST.fa");
print F "$fasta";
close F;

}

# TGILC

chdir "$resdir";
`$tgicl $resdir/castorEST.fa -c $cpu -l 40 -p 94 -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)

# 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

#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Open a results folder of TGICL
# -> parse the contigs and singlets
# -> Output as multifasta of single file
# Author: Rajkumar <r@rajkumar.in>
# Release SEP 2010 | For Rajendrakumar
# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SeqIO;
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 $curdir = "$path/user/rk/castor/unigene";
my $resdir = "$curdir/result";
my $data = "$resdir/castorEST.fa";
my $pardir = "$curdir/parsed";
my $cdbyank = "$path/tgicl/bin/cdbyank";

my ($i, $total, $file) = $_;
my @files = @_;

#Multi-threading
my $midstop = "0";
my $pm = new Parallel::ForkManager(4);

# making the parsed folder

if (-e "$pardir") {`rm -fr $pardir`;}
if (! -e "$pardir") {`mkdir $pardir`;}

# getting into the results folder

opendir (DIR, "$resdir") or die $!;
@files = readdir(DIR);
close(DIR);

my $c_files = @files - 2;

$i = 0;
foreach my $file(@files) {
next if ($file eq "." or $file eq "..");
next if ($file !~ m/^asm/);
#print "$file";
#next if (! -e "$resdir/$file/contigs");

$i++;

# Getting the contigs
my $in = Bio::SeqIO->new(-file => "$resdir/$file/contigs", -format => 'Fasta');
my ($identifier, $sequence) = $_;
while ( my $seq = $in->next_seq() ) {
$identifier = $seq->id;
$sequence = $seq->seq;

my $count_seq = length($sequence);
my $fasta = ">".$identifier."_Size:".$count_seq."bp\n".$sequence."\n";

open (F, ">>".$pardir."/contigs");
print F "$fasta";
close F;
}

}

# Fetching singlets
`$cdbyank $data.cidx <$data.singletons >$pardir/singlets.fa `;

# 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>

TGICL assembly - Revision history

Raj: Created page with 'Category:Bioinformatics * Assembling ~50000 ESTs ** Took 3.5 hours under 8 core ** both run and parse scripts are below #! /usr/bin/perl -w # *********…'

Raj: Created page with 'Category:Bioinformatics * Assembling ~50000 ESTs Took 3.5 hours under 8 core both run and parse scripts are below #! /usr/bin/perl -w # *********…'