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

2010-03-02T04:52:59Z

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

New page

[[Category: Bioinformatics]]

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

# *************************************************************
# This Programme does the following in sequence
# -> Performs regular Blast
# -> Modyfy the infile and outfile
# Author : Rajkumar (itc@rajkumar.in)
# lease: MAR 2010
# *************************************************************

# 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 $db = "$path/tobacco/data/blastdb/est_contig";
my $query = "$path/tobacco/data/tobea_unigene.fa";
my $outfile = "$path/tobacco/blast/tobea/tobea_est.blast.out";

my $blastdir = "$path/tobacco/blast/tobea";
my $multifastadir = "$blastdir/multifasta";
my $blastoutdir = "$blastdir/blastout";

my $cpu = "4";
my $i= $_;

# Functions

print "\n\tCreating required folders..\n";
# Having the required dir
if (-e "$multifastadir") {`rm -fr $multifastadir`;}
if (! -e "$multifastadir") {`mkdir $multifastadir`;}
if (-e "$blastoutdir") {`rm -fr $blastoutdir`;}
if (! -e "$blastoutdir") {`mkdir $blastoutdir`;}

my $total = `grep -c ">" $query`;
chomp $total;

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

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

my $c_sequence = length($sequence);
$identifier = $identifier."_".$c_sequence;

my $fasta = ">$identifier\n$sequence\n";

$i++;
my $math = $total - $i;

open (FASTA, ">".$multifastadir."/".$identifier);
print FASTA $fasta;
close FASTA;

print "\r\tInitiated Blast on $identifier [$math to go..]";
`blastall -p blastn -d $db -i $multifastadir/$identifier -e 10 -m 9 -q -3 -v 3 -o $blastoutdir/$identifier -a $cpu`;
print " done.";

# -p program
# -d database
# -i query file
# -e evalue
# -m 8 tab delimited out
# -o outfile
# -a number of CPUs
# -q Penalty for a nucleotide mismatch (blastn only) default = -3
# -v Number of database sequences to show one-line
# -K Number of best hits from a region to keep

}

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

print "All Done!\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>

Blast tobea - Revision history

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