[Bioperl-l] how to "tile" the HSPs of a hit-object ?
haralds_listen at gmx.de
Mon Mar 20 15:14:21 EST 2006
I want to use Bioperl for doing some psi-blast postprocessing (under
linux with bioperl 1.5 and perl 5.8.7).
For doing so I would like to get for every hit-sequence its alignment
with the query. So I dont want all those overlapping HSPs, but the one
and only alignment with best score.
I am reading in the documentation for that for some time and think, that
"tiling" is what I want to do to each hit-object.
As far as I have understood the documentation, calling
Bio::Search::SearchUtils::tile_hsps($hit); (or calling
$hit->ambiguous_aln(), which will call the aforementioned)
should be suficient so that $hit will become tiled. Right?
But if I run the following program, the ranges of the hsp-objects will
still overlap :-( - no matter if I use tile_hsp($hit) or
my $report = new Bio::SearchIO('-file'=>'out.txt',
my $result = $report->next_result;
my $iterat = $result->next_iteration;
while( my $hit = $iterat->next_hit )
while( my $hsp = $hit->next_hsp )
my @q_range = $hit->range('query');
my @h_range = $hit->range('hit');
$, = " ";
print "-" x 5, "\n";
Can anyone tell me where my problem lies?
Regards and thanks in advance,
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