Raj at 11:28, 16 July 2010

2010-07-16T11:28:50Z

← Older revision		Revision as of 11:28, 16 July 2010
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	<source lang=perl>		<source lang=perl>
	#! /usr/bin/perl -w		#! /usr/bin/perl -w

	# *************************************************************		# *************************************************************
	# This Programme does the following in sequence		# This Programme does the following in sequence
	# -> ~~Performs regular Blast~~		# -> Parses a multi fasta
	# -> ~~Infile~~ as ~~folder and write the progress~~		# -> Removes the sequence if they have <50bp and of 'N'
			# -> Capured as individual files.
	# Author : Rajkumar (itc@rajkumar.in)		# Author : Rajkumar (itc@rajkumar.in)
	# Release: JUL 2009		# Release: JUL 2009
Line 16:		Line 16:
	use Bio::Perl;		use Bio::Perl;
	use Bio::SeqIO;		use Bio::SeqIO;
	~~use Parallel::ForkManager;~~

	~~# At the top: Time Start~~
	~~my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);~~

	# Variables		# Variables
	my $path = "/home/raj/bio";		my $path = "/home/raj/bio";
	my $path1 = "$path/user/raja";		my $path1 = "$path/user/raja";
	my $path2 = "$path1/blast/BES-NR";		my $path2 = "$path1/blast/BES-NR";
	my $multifasta = "$path2/BES.fa";		my $multifasta = "$path2/BES.fa";
	my $~~infiledir~~ = "$path2/multifasta";		my $resdir = "$path2/multifasta";
	~~my $outdir = "$path2/blastout";~~

	~~my $db = "$path/data/nr/nr";~~


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


	~~# Multi-threading~~
	~~my $midstop = "16"; # If midstop is 0 it deals with all the files~~
	~~my $cpu = "1";~~
	~~my $pm = new Parallel::ForkManager(16)~~;

	# Getting the Grip of folders		# Getting the Grip of folders
	if (-e $~~outdir~~ ) {`rm -fr $~~outdir~~`;}		if (-e $resdir) {`rm -fr $resdir`;}
	if (! -e $~~outdir~~) {`mkdir $~~outdir~~`;}		if (! -e $resdir) {`mkdir $resdir`;}


	~~# Functions~~

	~~opendir~~ (~~DIR,~~ "$~~infiledir~~") ~~or die $!~~;		# making several Fasta files of GDNA
	~~@files = readdir(DIR)~~;		my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
	~~close(DIR)~~;		my $identifier;
			my $sequence;

	my $~~c_files~~ = ~~@files~~ - 2;		while ( my $seq = $in->next_seq() ) {
			$identifier = $seq->id;
	$i = 0;		$sequence = $seq->seq;
	~~foreach my~~ $~~file(@files) {~~
	~~next if (~~$~~file eq "." or $file eq "..")~~;		#Trim the identifier
	$i++;		$identifier =~ s/_Size:[0-9]+bp//g;

	if ($~~i > $midstop~~) ~~{last };~~		my ($fasta) = $_;
			$fasta = ">$identifier\n$sequence\n";
	~~$pm->start and next;~~

	~~my $percent~~ = ($~~i/$c_files)*100~~;
	$~~percent~~ = ~~sprintf(~~"~~%.2f",~~ $~~percent);~~

	~~print "\r~~\~~tInitiated [$i of $c_files] \|~~ $~~percent% ";~~
	~~chdir $infiledir;~~
	~~`blastall -p blastx -d $db -i $file -m 9 -o $outdir/~~\~~/$file.out -a $cpu`;~~
	~~# -p program~~
	~~# -d database~~
	~~# -i query file~~
	~~# -e evalue~~
	~~# -m 8 tab delimited out~~
	~~# -o outfile~~
	~~# -a number of CPUs~~
	~~# -q Penalty for a nucleotide mismatch (blastn only) default = -3~~
	~~# -v Number of database sequences to show one-line~~
	~~# -K Number of best hits from a region to keep~~
	~~print "Done.~~";
	~~$pm->finish~~;

	}		my $count_seq = length($sequence);
			my $count_N = ($sequence =~ tr/N//);
			my $math = $count_seq * 0.2;

			$sequence =~ s/-/N/;
			if ($count_seq < 50){ next; }
			if ($count_N > $math){ next; }

			open (FASTA, ">".$resdir."/".$identifier.".fa");
			print FASTA $fasta;
			close FASTA;

	~~$pm->wait_all_children;~~		# print "$identifier\t$count_seq\n";

	print "\~~nAll 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		# END


	</source>		</source>

Raj: Created page with 'Category: Bioinformatics #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in seque…'

2010-07-16T11:28:12Z

Created page with 'Category: Bioinformatics <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in seque…'

New page

[[Category: Bioinformatics]]

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

# *************************************************************
# This Programme does the following in sequence
# -> Performs regular Blast
# -> Infile as folder and write the progress
# Author : Rajkumar (itc@rajkumar.in)
# Release: JUL 2009
# *************************************************************

# 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 $path1 = "$path/user/raja";
my $path2 = "$path1/blast/BES-NR";
my $multifasta = "$path2/BES.fa";
my $infiledir = "$path2/multifasta";
my $outdir = "$path2/blastout";

my $db = "$path/data/nr/nr";

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

# Multi-threading
my $midstop = "16"; # If midstop is 0 it deals with all the files
my $cpu = "1";
my $pm = new Parallel::ForkManager(16);

# Getting the Grip of folders
if (-e $outdir ) {`rm -fr $outdir`;}
if (! -e $outdir) {`mkdir $outdir`;}

# Functions

opendir (DIR, "$infiledir") 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 "..");
$i++;

if ($i > $midstop) {last };

$pm->start and next;

my $percent = ($i/$c_files)*100;
$percent = sprintf("%.2f", $percent);

print "\r\tInitiated [$i of $c_files] | $percent% ";
chdir $infiledir;
`blastall -p blastx -d $db -i $file -m 9 -o $outdir/\/$file.out -a $cpu`;
# -p program
# -d database
# -i query file
# -e evalue
# -m 8 tab delimited out
# -o outfile
# -a number of CPUs
# -q Penalty for a nucleotide mismatch (blastn only) default = -3
# -v Number of database sequences to show one-line
# -K Number of best hits from a region to keep
print "Done.";
$pm->finish;

}

$pm->wait_all_children;

print "\nAll 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>

Trim multifasta.pl - Revision history

Raj at 11:28, 16 July 2010

Raj: Created page with 'Category: Bioinformatics #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in seque…'