Raj at 02:47, 8 May 2010

2010-05-08T02:47:21Z

← Older revision		Revision as of 02:47, 8 May 2010
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	# *************************************************************		# *************************************************************
	# This Programme does the following in sequence		# This Programme does the following in sequence
	# -> ~~Assembles ITC~~ and ~~TOEA ESTs~~		# -> Parses the TGCL results and assembles as singlets and contigs
	# -> ~~Multicored~~		# -> single cored
	# Author : Rajkumar (itc@rajkumar.in)		# Author : Rajkumar (itc@rajkumar.in)
	# Release: ~~APR~~ 2010		# Release: MAY 2010
	# *************************************************************		# *************************************************************

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	use Bio::SearchIO;		use Bio::SearchIO;
	use Parallel::ForkManager;		use Parallel::ForkManager;


	# At the top: Time Start		# At the top: Time Start
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	# Variables		# Variables
	my $path = "/home/raj/bio";		my $path = "/home/raj/bio";
	my $~~datadir~~ = "$path/tobacco/data";		my $curdir = "$path/tobacco/data";
	my $~~est~~ = "$~~datadir~~/~~est.fa~~";		my $resdir = "$curdir/unigene_result";
	my $resdir = "$~~datadir~~/~~unigene_result~~";		my $singlets = "$resdir/singlets";
			my $contigs = "$resdir/contigs";
	my $~~tgicl~~ = "$~~path~~/~~tgicl/tgicl~~";		my $singlets_temp = "$resdir/singlets_temp";
	my $~~cpu~~ = "16";		my $contigs_temp = "$resdir/contigs_temp";
			my $unigenes = "$curdir/unigenes.fa";


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

	# Clear the Files		# Clear the Files

	if (-e "$~~resdir~~") {`rm -fr $~~resdir~~`;}		if (-e "$singlets") {`rm $singlets`;}
	if (! -e "$~~resdir~~") {`~~mkdir~~ $~~resdir~~`;}		if (-e "$contigs") {`rm $contigs`;}
			if (-e "$singlets_temp") {`rm $singlets_temp`;}
			if (-e "$contigs_temp") {`rm $contigs_temp`;}
			if (-e "$unigenes") {`rm $unigenes`;}


	# Parsing the Contigs		# Parsing the Contigs
	~~chdir~~ "$resdir";
	`$~~tgicl~~ $~~est~~ -c $~~cpu~~ -~~l 40~~ -~~p 94~~ -M`;		opendir (DIR, "$resdir") or die $!;
	# -~~l miminum overlap length~~ (~~default 40~~)		@asm = readdir(DIR);
	# -~~M ignore lower~~-~~case masking~~ in ~~<fasta_db~~> ~~sequences~~		close(DIR);
	# -~~p minimum percent identity for overlaps <PID~~> (~~default 94~~)
			foreach my $asm (@asm) {
			if ($asm !~ m/^asm_/) {next;}

			`cat $resdir/$asm/contigs >>$contigs_temp`;
			`cat $resdir/$asm/singlets >>$singlets_temp`;
			}


			# Renaming and Writing the final Unigenes (contigs)

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

			while ( my $seq = $in->next_seq() ) {
			$identifier = $seq->id;
			$sequence = $seq->seq;

			$identifier = "UNI_CON_".$identifier;

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

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

			}


			# Renaming and Writing the final Unigenes (singlets)

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

			while ( my $seq = $in->next_seq() ) {
			$identifier = $seq->id;
			$sequence = $seq->seq;

			$identifier = "UNI_SIN_".$identifier;

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

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

			}

	print "\n\tAll Done!\n\n";		print "\n\tAll Done!\n\n";

	# At the End: Time Calculation		# At the End: Time Calculation
	my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);		my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);
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	# END		# END


	</source>		</source>

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

Raj: Created page with ' #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Assembles ITC and TO…'

2010-04-30T06:26:13Z

Created page with '<source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Assembles ITC and TO…'

New page

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

# *************************************************************
# This Programme does the following in sequence
# -> Assembles ITC and TOEA ESTs
# -> Multicored
# 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 $est = "$datadir/est.fa";
my $resdir = "$datadir/unigene_result";

my $tgicl = "$path/tgicl/tgicl";
my $cpu = "16";

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

# Clear the Files

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

# Parsing the Contigs
chdir "$resdir";
`$tgicl $est -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)
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
</source>

[[Category: Bioinformatics]]

Parse assemblage ITC EST-TOBEA EST - Revision history

Raj at 02:47, 8 May 2010

Raj: Created page with ' #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Assembles ITC and TO…'