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Gmane
From: WoA <witch.of.agnessi <at> gmail.com>
Subject: Missing Method: "get_tiled_alns"
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 29th April 2013 21:55:01 UTC (over 3 years ago)
Hi All,

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,  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 @alns = $tiling->get_tiled_alns('abc123');
 
my $concat_seq_obj = $alns[0]->get_seq_by_id('abc123');


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