Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the co-ordinates files #...

2009-12-29T20:08:56Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the co-ordinates files #...

New page

<source lang=perl>

#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Parse the co-ordinates files
# -> Select the scaffolds
# -> Mark the specific region
# -> Add 300bp on both the sides
# -> Fetch the scaffolds as fasta and then as a multifasta
# 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 $scafdir = "$path/euca/data/grandis/scaffold/trim";
my $blastdir = "$path/euca/blast";
my $resdir = "$blastdir/scaffold";
my $scaf_coor = "$blastdir/scaf_coor_curated.stat";
my $addbp = "300";
my $scaf_ssr_dir = "$path/euca/data/grandis/scaffold/ssr";
my $scaf_ssr = "$scaf_ssr_dir/scaf_ssr.fa";

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

# Parsing Functions

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

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

my ($scaf_id, $start, $end) = split(/\t/, $line);

# Adding 300bp on both the sides
my $length = ();
my $math = $start-$addbp;
if ($math > 0) {
$start = $start - $addbp;
$length = $end - $start + $addbp;
}

else {
$length = $end - $start + $addbp;
}

# Get the scaffolds
opendir (DIR, "$scafdir") or die $!;
@files = readdir(DIR);
close(DIR);
foreach my $file(@files) {
next if ($file !~ m/$scaf_id.txt/g);

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

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

$identifier = "GRAN_".$identifier;
$sequence = substr($sequence, $start, $length);

my $fasta = ">$identifier\n$sequence\n";
open (FH, ">>".$resdir."/".$file);
print FH "$fasta";
close FH;

print "\tWritten $scaf_id\n"

}
}

}

# Make a multifasta of results file
opendir (DIR, "$resdir") or die $!;
@files1 = readdir(DIR);
close(DIR);
foreach my $file1(@files1) {
next if ($file1 eq "." or $file1 eq "..");
push(@array, "$file1");

chdir $resdir;
`cat @array >$scaf_ssr`;

}

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
</perl>

Fetch scaf.pl - Revision history

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the co-ordinates files #...