Raj at 05:24, 28 October 2016

2016-10-28T05:24:06Z

← Older revision		Revision as of 05:24, 28 October 2016
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			[[Category:Bioinformatics]]

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

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the parsed Blast output o...

2009-12-29T17:43:31Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the parsed Blast output o...

New page

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

# *************************************************************
# This Programme does the following in sequence
# -> Parse the parsed Blast output of scaffold mapping
# -> Get the hit co-ordinates for each scaffold
# -> The co-ordinate window of EST-scaffolds map that have only 3kb in length
# -> Write the results as scaffold and co-ordinate window
# -> Pick out the selected scaffold sequences only with that co-ordinate window
# -> Some scaffolds have distinct hits at more than 1 places and will written as separate file. They need to cured manyually.
# Author : Rajkumar (itc@rajkumar.in)
# Release: DEC 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 $datadir = "$path/euca/blast/result";
my $coordir = "$path/euca/blast/coor";
my $blastdir = "$path/euca/blast";
my $scaf_coor = "$blastdir/scaf_coor.stat";
my $scaf_coor1 = "$blastdir/scaf_big_coor.stat";

my ($i) = $_;
my (@files, @files1) = @_;

# Parsing Functions

# Having the required dir
if (-e "$coordir") {`rm -fr $coordir`;}
if (! -e "$coordir") {`mkdir $coordir`;}
if (-e "$scaf_coor") {`rm $scaf_coor`;}
if (-e "$scaf_coor1") {`rm $scaf_coor1`;}

opendir (DIR, "$datadir") or die $!;
@files = readdir(DIR);
close(DIR);

foreach my $file(@files) {
next if ($file eq "." or $file eq "..");

# Clearing the array
my (@coor, @coordata) = ();
my $scaf_id = ();
my $est_id = ();

foreach my $line (split ("\n", `cat $datadir/$file`)) {

my ($junk1, $junk2, $junk3, $aln_length, $junk5, $junk6, $junk7, $junk8, $start, $end) = split(/\t/, $line);
push(@coor, "$start", "$end");
$scaf_id = "$junk2";
$est_id = "$junk1";
}

# manipurate the array (arrange)
@coor = sort({$a <=> $b}@coor);
my $math = $coor[-1] - $coor[0];
next if ($math >5000);
next if ($math <150);

my $tempfile = "$scaf_id\t$coor[0]\t$coor[-1]\n";
open (FH, ">>".$coordir."/".$scaf_id);
print FH "$tempfile";
close FH;
}

# Further filtering the co-ordinates because there are many same scaffolds
opendir (DIR, "$coordir") or die $!;
@files1 = readdir(DIR);
close(DIR);

foreach my $file1(@files1) {
next if ($file1 eq "." or $file1 eq "..");

# Clearing the array
my (@coor1, @coordata1) = ();
my $scaf_id1 = ();

foreach my $line1 (split ("\n", `cat $coordir/$file1`)) {

my ($junk, $start1, $end1) = split(/\t/, $line1);
push(@coor1, "$start1", "$end1");
$scaf_id1 = "$junk";

}

# manipurate the array (arrange)
@coor1 = sort({$a <=> $b}@coor1);
my $math1 = $coor1[-1] - $coor1[0];

if ($math1 <5000) {

my $tempfile1 = "$scaf_id1\t$coor1[0]\t$coor1[-1]\n";
open (FH, ">>".$scaf_coor);
print FH "$tempfile1";
close FH;
}

else {

my $tempfile2 = "$scaf_id1\t@coor1\n";
open (FH, ">>".$scaf_coor1);
print FH "$tempfile2";
close FH;
}
}

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>

Co-ordinates blast.pl - Revision history

Raj at 05:24, 28 October 2016

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the parsed Blast output o...