Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open the misa results # -> Pa...

2009-12-30T10:35:50Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open the misa results # -> Pa...

New page

<source lang=perl>

#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Open the misa results
# -> Parse the files
# -> compare the original EST file and pick the sequence that have repeats
# -> Outputs as fasta
# Author: Rajkumar (itc@rajkumar.in)

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

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

# Variables
my $path = "/home/raj/bio";
my $ssrdir = "$path/euca/ssr";
my $datadir = "$ssrdir/data";
my $resdir = "$ssrdir/result";

my $est = "$datadir/globulus_est_trim.fa";
my $repeat = "$resdir/globulus_est_trim.fa.misa";
my $resfile = "$datadir/globulus_est_repeat.fa";

my ($i, $ssr_id, $total, $math ) = $_;
my (@repeat_id, @identifier) = @_;

# Function

# Lets Clean it
if (-e "$resfile") {`rm $resfile`;}

# start your hack

open(CSV, "$repeat") or die "Idiot! Where is that Misa Outfile ? 'CSV': $!\n";
<CSV>; # skip header line
while (my $line = <CSV>) {

my ($ssr_id) = split('\t', $line);
next if ($ssr_id =~ m/^ID/);

push (@repeat_id, "$ssr_id");
}

# Making them Unique
my %seen;
my @unique_repeat_id = grep !$seen{$_}++, @repeat_id;

# Getting some statistics
my $count_unique_repeat_id = @unique_repeat_id;
$i = 0;

# Lets Grab the sequence
foreach my $repeat_id(@unique_repeat_id) {

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

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

next if ($repeat_id ne $identifier);

if ($repeat_id eq $identifier) {

my $fasta = ">$identifier\n$sequence\n";
open (FH, ">>".$resfile);
print FH $fasta ;
close FH ;
print "\r\tWritten $identifier. Still $i of $count_unique_repeat_id to be written!";
}
}
}

print "\n\tDone All Man\nOutfile written into $resfile\n\n";

# END

</source>

Parse misa1.pl - Revision history

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open the misa results # -> Pa...