Mark A. Jensen | 30 Apr 18:43 2013
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Re: Missing Method:"get tiled alnnns"

That was probably a beta method (though it has tests). Not being around much, I couldn't tell you details,
but you can find the code (you would need all the modules here) at 
https://github.com/bioperl/bioperl-live/tree/8164a826a4366ad3ec56c33cadfd9f0639262217/Bio/Search/Tiling

MAJ

>-----Original Message-----
>From: WoA [mailto:witch.of.agnessi <at> gmail.com]
>Sent: Monday, April 29, 2013 05:56 PM
>To: Bioperl-l <at> lists.open-bio.org
>Subject: [Bioperl-l]  Missing Method: &quot;get_tiled_alns&quot;
>
>
>I'm trying to get alignment from tiled information generated out of a Blastx
>report, (for two sequences made by 'blas2seq'). I'm using ActivePerl  15.6.2
>and Bioperl 1.6 in Windows 7
>
>However I'm getting the following error:
>
>Can't locate object method "get_tiled_alns" via package
>"Bio::Search::Tiling::Ma
>pTiling" at tile_align_blastx.pm line 11, <GEN1> line 72.
>
>
>
>
>The code is as follows:
>
>use strict;
>use warnings;
>use Bio::SearchIO;
>use Bio::Search::Tiling::MapTiling;
>
>my $blio = Bio::SearchIO->new( -file => 'test.blastx2seq.out', -format
>=>'blast');
>my $result = $blio->next_result;
>my $hit = $result->next_hit;
>my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
>my  <at> alns = $tiling->get_tiled_alns('abc123');
> 
>my $concat_seq_obj = $alns[0]->get_seq_by_id('abc123');
>
>
>-- 
>View this message in context: http://old.nabble.com/Missing-Method%3A-%22get_tiled_alns%22-tp35347933p35347933.html
>Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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Gmane