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Old 08-24-2015, 09:27 AM   #1
swttalyan
Junior Member
 
Location: Germany

Join Date: Aug 2015
Posts: 1
Thumbs up Blast HSP tiling BioPerl Module Query

Hi,

Greetings!

I have one query regarding HSP tiling. I want to parse tblastn output to merge all overlapping HSPs and also non-overlaping HSP with some distance cutoff and would like to get every possible statics which blast tabular format provides.

What i have written untill now. but i dont have much experience with Bioperl blast tiling. Could you please help me with the same?


use Bio::SearchIO;

use Bio::Search::Tiling::MapTiling;
use Bio::Search::Tiling::TilingI;
open (FH,">trial_output.txt");
my $in = new Bio::SearchIO(-format => 'blast',
-file => 'output.tblastn');
while( my $result = $in->next_result ) {
## $result is a Bio::Search::Result::ResultI compliant object
while( my $hit = $result->next_hit ) {
## $hit is a Bio::Search::Hit::HitI compliant object


$tiling = Bio::Search::Tiling::MapTiling->new($hit);
my $ident = $tiling->identities('query','exact');
$query_length = $tiling->length('query');
#print $query_length."\t";
#print $ident."\t";
#print $result-> query_name,"\t";



my @contexts = $tiling->contexts('query');
my $best_context = pop @contexts;
my $max_frac = $tiling->frac_conserved(-type=>'query',
-action=>'exact',
-context=>$best_context);

my $max_identical = $tiling->frac_identical(-type=>'query',
-action=>'exact',
-context=>$best_context);

my $range = $tiling->range('query',$best_context);

#@alns = $tiling->get_tiled_alns('query', $best_context);

my @map = $tiling->coverage_map_as_text('query', $best_context);


foreach $m (@map)
{
print $m."\t";
}
print $max_frac."\t".$max_identical."\t".$range."\n";
}
}


Best,
Sweta
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bioinformatics, bioperl, blast, hsp tiling

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