[Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie now available BETA

Mark A. Jensen maj at fortinbras.us
Mon Feb 22 14:07:29 EST 2010

It's actually seems to work pretty well so far--validation on xsd + integration 
wrapperbase/commandexts. One does:

use Bio::Tools::WrapperMaker;

$fac = Bio::Tools::WrapperMaker->compile( -defs => 'samtools.xml' );

$fac->set_parameters( -command => 'view', -bam_out => 1, -sam_in => 1);
$fac->run( -bam => 'my.sam', -out => 'my.bam');

or put it in a namespace

Bio::Tools::WrapperMaker->compile( -defs => 'samtools.xml', -namespace => 

$fac = My::Samtools->new();

I've been working on a WrapperMaker defs editor
at Fortinbras so people don't have to write XML.
Tuits are in short supply lately, but I'm thinking this might be a
good Summer O Code project...
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>; "Ben Bimber" <bimber at wisc.edu>
Sent: Monday, February 22, 2010 1:46 PM
Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie 
now available BETA

> On Mon, 2010-02-22 at 12:53 -0500, Mark A. Jensen wrote:
>> ... I'm secretly working on is a package called WrapperMaker, that uses XML
>> based on an XML Schema to define program names, commands, inputs and other
>> details
>> (rather than an ugly Config module exporting hard to remember global 
>> variables),
>> passing them to CommandExts and providing a nice WrapperBase object
>> transparently. This is getting there, but isn't ready for primetime.)
>> cheers MAJ
> Sounds promising; I could foresee having a config-file based approach
> usable across other Bio* languages; they would just need to come up with
> similar wrappers and parsers.  Might be something to bring up with the
> biopython/bioruby crowd.
> Also, have you thought about possibly abstracting out parts so that one
> could describe the relevant bits in alternative formats (JSON, YAML,
> etc) other than XML?  Something like this might be handy:
> http://search.cpan.org/~bricas/Config-Any-0.19/
> chris
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