[Bioperl-l] not able to use Bio::Root::IO method

Mark A. Jensen maj at fortinbras.us
Thu Jan 14 00:11:01 EST 2010


Hey Dan-- what does your constructor look like? I wonder if something's getting 
lost in new() and _initialize() chaining spaghetti- MAJ
----- Original Message ----- 
From: "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, January 13, 2010 11:26 PM
Subject: [Bioperl-l] not able to use Bio::Root::IO method


> Hi All,
>
> I'm having a stupid problem that for some reason I just can't figure
> out. I'm putting together a B:A:IO:bowtie module to wrap around the
> B:A:IO:sam module so bowtie output can be used as an assembly start
> point.
>
> For some reason that is escaping me I can't create tempfiles!
>
> What should be the relevant code in the module:
>
> package Bio::Assembly::IO::bowtie;
> use strict;
> use warnings;
>
> # Object preamble - inherits from Bio::Root::Root
>
> use Bio::SeqIO;
> use Bio::Tools::Run::Samtools;
> use Bio::Assembly::IO;
> use Carp;
> use Bio::Root::Root;
> use Bio::Root::IO;
> use base qw( Bio::Root::Root Bio::Root::IO Bio::Assembly::IO );
>
>
> and the line (there are a couple of others that are like to fail in the
> same way, but I've not got that far)
>
> my ($sam_tmp_h, $sam_tmp_f) = $self->io->tempfile( -dir =>
> $self->tempdir(), -suffix => '.sam' );
>
> Which dies with:
> Can't locate object method "io" via package "Bio::Assembly::IO::bowtie"
> at /usr/local/share/perl/5.10.0/Bio/Assembly/IO/bowtie.pm line 175.
>
> Relevant environment vars:
>  DB<10> x @ISA
> 0  'Bio::Root::Root'
> 1  'Bio::Root::IO'
> 2  'Bio::Assembly::IO'
>
> DB<11> x $self
> 0  Bio::Assembly::IO::bowtie=HASH(0x2d226d8)
>   '_no_head' => undef
>   '_no_sq' => undef
>   '_root_verbose' => 0
>
>
>
> Can someone suggest what I'm missing?
>
> cheers
> Dan
>
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