[Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report.

[Mark A. Jensen]

Hi Fred-
I've been looking hard at this; my guess is it's a bug in relating
strand/frame contexts to the 'all' AA-only context.
Would be kind enough to submit a bug report to
http://bugzilla.bioperl.org
and attach your script and the blast report?
I will work on this ASAP.
Thanks
Mark
----- Original Message ----- 
From: <Frederic.SAPET at biogemma.com>
To: <bioperl-l at bioperl.org>
Sent: Friday, October 30, 2009 6:10 AM
Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report.


> Hello
>
> I'm trying to use the new  Bio::Search::Tiling::MapTiling (I have tried
> both BioPerl 1.6.1 and the last nightly build)  module on a WuBlastX
> report after reading the documentation
> (http://www.bioperl.org/wiki/HOWTO:Tiling).
> Please find in attachment the sample file I used for my test.
>
>
>
>
> Here is the code I have tried :
>
> use Bio::SearchIO;
> use Bio::Search::Tiling::MapTiling;
>
> my $blio = Bio::SearchIO->new( -format => 'blast',
>                                     -file => 'WuBlastX.txt'
> );
>
> my $result = $blio->next_result;
>
> while (my $hit = $result->next_hit) {
>    my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
>    my @contextsQ = $tiling->contexts('query');
>        for my $contextQ ( @contextsQ ) {
>        my ($min, $max) = $tiling->range('query', $contextQ);
>        my $tLengthQ = $tiling->length('query', 'exact', $contextQ);
>                print "QUERY range in *$contextQ* => $min, $max
> (length=$tLengthQ)\n";
>        }
>        my @contextsS = $tiling->contexts('subject');
>        for my $contextS ( @contextsS ) {
>        my ($min2, $max2) = $tiling->range('subject', $contextS);
>                print "SUBJECT range in *$contextS* => $min2, $max2\n";
>        }
> }
>
> exit;
>
> Results printed on my terminal are :
>
> QUERY range in *m1* => 4065, 10571 (length=7038)
> QUERY range in *m0* => 7, 11037 (length=2577)
> QUERY range in *m2* => 2462, 14599 (length=327)
> SUBJECT range in *all* => 435, 270
>
> I think that the right query range in m1 context should be 1170 to 10571
> (and length 6828 ?)
> and subject range has to be 231 to 3563 no ?
>
> The m1 context seems to be the best one, with 2271 amino acid aligned  (in
> 4 HSP )between MySampleSeq and the Protein B9GCX0.
>
> Could you please help me to point what is wrong ?
>
> Thank you.
>
> Fred


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