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

2010-06-03T14:16:40Z

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

New page

[[Category:Bioinformatics]]
<source lang=perl>
#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Count Numbers and generate statistics
# -> Singlecored
# Author : Rajkumar (itc@rajkumar.in)
# Release: JUN 2010
# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SearchIO;
use List::Util qw[min max];
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 $curdir = "$path/tobacco/annotation/gt";

my $infile = "$datadir/unigenes.fa";
my $outfile = "$curdir/est.stat";

my ($i, $c_fasta) = $_;
my (@length) = @_;

my $pm = new Parallel::ForkManager(16);

# Genome threader RUN

print "\n\tCounting ...\n";

# count number of fasta
$c_fasta = `grep -c ">" $infile`;
chomp $c_fasta;

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

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

$i++;

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

my $length = ($sequence =~ tr/[A-Z]|[a-z]//);

push(@length, "$length");

#print "$identifier\t$length\n";

}

my $mini = min(@length);
my $maxi = max(@length);
my $c_array = @length;

my $set1 = @length[$mini .. 1000];
my $set2 = @length[1001 .. 2000];
my $set3 = @length[2001 .. 3000];
my $set4 = @length[3001 .. $maxi];

print "Max:$maxi\tMini:$mini\tTotalLength:$c_array\n
Set1:$set1\tSet2:$set2\tSet3:$set3\tSet4:$set4\n";

exit;

# 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>

Count fasta.pl - Revision history

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