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

2010-04-14T05:49:52Z

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

New page

[[Category: Bioinformatics]]

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

# *************************************************************
# This Programme does the following in sequence
# -> Parse the Blast output of scaffold mapping
# -> Write the results into a seperate folder with each identifier
# -> Write the statistics files (est_scaf_hit.stat, unique_scaf_hit.stat)
# Author : Rajkumar (itc@rajkumar.in)
# Release: APR 2009
# *************************************************************

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

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

# Variables
my $path = "/home/raj/bio";
my $infile = "$path/user/rk/pmapping/est_sorghum.blast.out";
my $tempdir = "$path/user/rk/pmapping/temp";
my $resdir = "$path/user/rk/pmapping/result";

my ($i) = $_;
my (@files) = @_;

# Parsing Functions

# Having the required dir
if (-e "$tempdir") {`rm -fr $tempdir`;}
if (! -e "$tempdir") {`mkdir $tempdir`;}
if (-e "$resdir") {`rm -fr $resdir`;}
if (! -e "$resdir") {`mkdir $resdir`;}

# Let's Parse the file to have files written for indiavidual ESTs

foreach my $line (split ("\n", `cat $infile`)) {

next if ($line !~ m/^PUT-/);

foreach my $tab (split ("\t", $line)) {
next if ($tab !~ m/^PUT/);

if ($tab =~ m/^PUT/) {

open (FH, ">>".$tempdir."/".$tab.".gff");
print FH "$line\n";
close FH;
}
}
}

# Work woth the temp file to pick only the top hits with one scaffold
opendir (DIR, "$tempdir") or die $!;
@files = readdir(DIR);
close(DIR);

foreach my $file(@files) {
next if ($file eq "." or $file eq "..");
$i = 0;
foreach my $line_ (split ("\n", `cat $tempdir/$file`)) {

# Filters only the top hit EST

$i++;
next if ($i>1);

open (F, ">>".$resdir."/est_sorghum.blast.tophit.out");
print F "$line_\n";
close F;
}
}

# cleaning the temp dir
if (-e "$tempdir") {`rm -fr $tempdir`;}

print "\nDone!\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>

Parse blast est-gdna sorghum.pl - Revision history

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