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

Chris Fields cjfields at illinois.edu
Thu Jan 14 02:25:05 EST 2010

Yes, that's true.  The call to an io() is a Bio::Tools::Run::WrapperBase thing (the io() is a Bio::Root::IO instance).


On Jan 13, 2010, at 11:38 PM, Mark A. Jensen wrote:

> up to list
> ----- Original Message ----- From: "Mark A. Jensen" <maj at fortinbras.us>
> To: "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
> Sent: Thursday, January 14, 2010 12:36 AM
> Subject: Re: [Bioperl-l] not able to use Bio::Root::IO method
>> Aha-- check out the pod for Bio::Root::IO:
>> "This module provides methods that will usually be needed for any sort
>> of file- or stream-related input/output, e.g., keeping track of a file
>> handle, transient printing and reading from the file handle, a close
>> method, automatically closing the handle on garbage collection, etc.
>> To use this for your own code you will either want to inherit from
>> this module, or instantiate an object for every file or stream you are
>> dealing with. In the first case this module will most likely not be
>> the first class off which your class inherits; therefore you need to
>> call _initialize_io() with the named parameters in order to set file
>> handle, open file, etc automatically."
>> I think you're wanting a call to $self->_initialize_io(). (There is no io() method explicitly defined in any of the base classes.)
>> MAJ
>> ----- Original Message ----- From: "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, January 13, 2010 11:26 PM
>> Subject: [Bioperl-l] not able to use Bio::Root::IO method
>>> Hi All,
>>> I'm having a stupid problem that for some reason I just can't figure
>>> out. I'm putting together a B:A:IO:bowtie module to wrap around the
>>> B:A:IO:sam module so bowtie output can be used as an assembly start
>>> point.
>>> For some reason that is escaping me I can't create tempfiles!
>>> What should be the relevant code in the module:
>>> package Bio::Assembly::IO::bowtie;
>>> use strict;
>>> use warnings;
>>> # Object preamble - inherits from Bio::Root::Root
>>> use Bio::SeqIO;
>>> use Bio::Tools::Run::Samtools;
>>> use Bio::Assembly::IO;
>>> use Carp;
>>> use Bio::Root::Root;
>>> use Bio::Root::IO;
>>> use base qw( Bio::Root::Root Bio::Root::IO Bio::Assembly::IO );
>>> and the line (there are a couple of others that are like to fail in the
>>> same way, but I've not got that far)
>>> my ($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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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