Parse sorghum genome.pl - Revision history

Raj at 07:38, 23 April 2011

2011-04-23T07:38:38Z

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Raj at 07:36, 23 April 2011

2011-04-23T07:36:31Z

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Raj at 07:23, 23 April 2011

2011-04-23T07:23:16Z

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Raj at 07:15, 23 April 2011

2011-04-23T07:15:39Z

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Raj at 06:34, 23 April 2011

2011-04-23T06:34:23Z

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Raj at 06:24, 23 April 2011

2011-04-23T06:24:14Z

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Raj at 16:35, 12 August 2010

2010-08-12T16:35:56Z

← Older revision		Revision as of 16:35, 12 August 2010
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			#! /usr/bin/perl -w
			# *************************************************************
			# This Programme does the following in sequence
			# -> Parses a multi fasta
			# -> Write each sequence as individual files
			# Author : Rajkumar (r@rajkumar.in)
			# Release: AUG 2010
			# *************************************************************

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

			# Variables
			my $path = "/home/raj/bio/user/rk/genome";
			my $multifasta = "$path/sb_genome.fa";
			my $resdir = "$path/individual_files_fasta";
			my $zipdir = "$path/individual_files_zip";
			my ($i,$file) = $_;
			my (@files) = @_;

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

			# Multi-threading
			my $midstop = "0"; # If midstop is 0 it deals with all the files
			my $pm = new Parallel::ForkManager(8);


			# Getting the grip of files
			if (-e "$resdir") {`rm -fr $resdir`;} if (! -e "$resdir") {`mkdir $resdir`;}
			if (-e "$zipdir") {`rm -fr $zipdir`;} if (! -e "$zipdir") {`mkdir $zipdir`;}

			# Let's Hack


			# count the fasta
			my $c_fasta = `grep -c ">" $multifasta`; chomp $c_fasta;

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

			$i = 0;
			while ( my $seq = $in->next_seq() ) {
			$identifier = $seq->id;
			$sequence = $seq->seq;
			$i++;

			$pm->start and next;


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


			my $count_seq = length($sequence);
			$count_seq = $count_seq/1000000;
			$count_seq = sprintf("%.2f", $count_seq);

			my $fasta = ">".$identifier."_Size:".$count_seq."Mb\n".$sequence."\n";
			my $id_size = $identifier."_Size:".$count_seq."Mb.fa";

			print "\n\tInitiated [$i of $c_fasta] \| $percent% ";

			open (FH, ">".$resdir."/".$id_size);
			print FH $fasta ;
			close FH ;


			chdir $resdir;
			`zip $zipdir/$id_size.zip $id_size`;

			$pm->finish;
			}

			$pm->wait_all_children;

			`rm -fr $resdir`;

			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>		</source>

Raj: Created page with 'Category:Bioinformatics '

2010-08-12T16:27:49Z

Created page with 'Category:Bioinformatics <source lang=perl> </source>'

New page

[[Category:Bioinformatics]]

<source lang=perl>

</source>