Raj: Created page with 'Category: Bioinformatics #!/usr/bin/perl -w # Libraries use Bio::SearchIO; use Parallel::ForkManager; # Variables my ($i) = $_; # Input prompt …'

2010-07-20T03:29:13Z

Created page with 'Category: Bioinformatics <source lang=perl> #!/usr/bin/perl -w # Libraries use Bio::SearchIO; use Parallel::ForkManager; # Variables my ($i) = $_; # Input prompt …'

New page

[[Category: Bioinformatics]]

<source lang=perl>

#!/usr/bin/perl -w

# Libraries
use Bio::SearchIO;
use Parallel::ForkManager;

# Variables
my ($i) = $_;

# Input prompt

if (! $ARGV[0]) {
print "What is the BLAST file to parse? ";
chomp ($inFile = <STDIN>);
}
else {
$inFile = $ARGV[0];
}

# Multithreading
my $pm = new Parallel::ForkManager(16);

# Some counting
my $c_entries = `grep -c "Sequences producing significant alignments" $inFile`;
chomp $c_entries;

# Making the outfile
open (GFF, ">".$inFile.".csv");
print GFF "Query\tHitName\tHitDesc\tHSP_rank\t\%ID\teValue\tHSP_length\n";
close GFF;

# Parsing Function
$report = new Bio::SearchIO(
-file=>"$inFile",
-format => "blast");

$i = 0;
# Go through BLAST reports one by one
while($result = $report->next_result) {

$i++;
$pm->start and next;

# Go through each each matching sequence
while($hit = $result->next_hit) {

# Go through each each HSP for this sequence
while ($hsp = $hit->next_hsp) {

# Capture the results
my $accesssion = $result->query_accession;
my $hitname = $hit->name;
my $HitDesc = $hit->description;
my $rank = $hsp->rank;
my $identity = $hsp->percent_identity;
my $evalue = $hsp->evalue;
my $hsp_length = $hsp->hsp_length;

#Conditions
next if $hsp->percent_identity < 80 ;
next if $hsp->hsp_length < 80 ;
$identity = sprintf ("%.2f", $identity);

# Writing into files
open (GFF, ">>".$inFile.".csv");
print GFF "$accesssion\t$hitname\t$HitDesc\t$rank\t$identity\t$evalue\t$hsp_length\n";
close GFF;

#Decorating the log
my $percent = ($i/$c_entries)*100;
$percent = sprintf("%.2f", $percent);

print "\n\tCompleted [$i of $c_entries] | $percent% ";

}
}

$pm->finish;
}
$pm->wait_all_children;

# END

</perl>

Parse BES-flaxESTs - Revision history

Raj: Created page with 'Category: Bioinformatics #!/usr/bin/perl -w # Libraries use Bio::SearchIO; use Parallel::ForkManager; # Variables my ($i) = $_; # Input prompt …'