Raj at 16:08, 4 January 2010

2010-01-04T16:08:49Z

← Older revision		Revision as of 16:08, 4 January 2010
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	<~~pre~~>		<source lang=perl>
	#! /usr/bin/perl -w		#! /usr/bin/perl -w
	# *************************************************************		# *************************************************************
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	# END		# END

	</~~pre~~>		</source>

Raj: New page:

 #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Write them as indiv...

2009-10-29T16:22:37Z

New page: <pre> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Write them as indiv...

New page

<pre>
#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> Write them as individual files
# Author: Rajkumar (itc@rajkumar.in)

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

# Libraries
use strict;
use Bio::Perl;
use Bio::SeqIO;

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

# Variables
my $path = "/home/raj/bio";
my $resdir = "$path/tobacco/mapping/gt/result/singlet";
my $multifasta = "$path/tobacco/data/singlet.fa";

my ($i, $total) = $_;

# Fetching the total number of Fasta sequences
$total = `grep -c ">" $multifasta`;
$total =~ s/\n//g;

# making several Fasta files of GDNA

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

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

my ($fasta) = $_;
$fasta = ">$identifier\n$sequence\n";
++$i;
if ($i < 100000){
if (! -e "$resdir/1") {`mkdir $resdir/1`;}
open (FASTA, ">".$resdir."/1/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 100000 && $i < 200000 ){
if (! -e "$resdir/2") {`mkdir $resdir/2`;}
open (FASTA, ">".$resdir."/2/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 200000 && $i < 300000 ){
if (! -e "$resdir/3") {`mkdir $resdir/3`;}
open (FASTA, ">".$resdir."/3/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 300000 && $i < 400000 ){
if (! -e "$resdir/4") {`mkdir $resdir/4`;}
open (FASTA, ">".$resdir."/4/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 400000 && $i < 500000 ){
if (! -e "$resdir/5") {`mkdir $resdir/5`;}
open (FASTA, ">".$resdir."/5/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 500000 && $i < 600000 ){
if (! -e "$resdir/6") {`mkdir $resdir/6`;}
open (FASTA, ">".$resdir."/6/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 600000 && $i < 700000 ){
if (! -e "$resdir/7") {`mkdir $resdir/7`;}
open (FASTA, ">".$resdir."/7/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 700000 && $i < 800000 ){
if (! -e "$resdir/8") {`mkdir $resdir/8`;}
open (FASTA, ">".$resdir."/8/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

if ( $i > 800000 ){
if (! -e "$resdir/9") {`mkdir $resdir/9`;}
open (FASTA, ">".$resdir."/9/".$identifier.".fa");
print FASTA $fasta;
close FASTA;
}

my $math = $total-$i;

print "\r\tYa. Written $identifier. Still $math to go..";

}

print "\t\nYES MAN.. All 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

</pre>

Multifasta-fastas - Revision history

Raj at 16:08, 4 January 2010

Raj: New page:
#! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Write them as indiv...