[Bioperl-l] Bio::Tools::Run::Cap3 usage question

Florent Angly florent.angly at gmail.com
Tue Nov 24 17:54:48 EST 2009

Hi Paolo,

It turns out that there is no standard for what is to be passed to the 
Bio::Tools::Run wrappers and returned by them. I noticed the 
inconsistency between the assembly wrappers recently while implementing 
support for new wrapper. I implemented inital support for additional de 
novo assembly programs in BioPerl (454 Newbler and Minimo) a couple of 
weeks ago and Mark Jensen added support for Maq, a program that 
assembler reads against a reference. In the process, all the assembly 
wrappers were changed to take the same type of input data (a FASTA 
sequence or an array reference of sequence objects) and return one of 
the following:
    * a Bio::Assembly::Scaffold object (the default), or
    * a Bio::Assembly::IO object, or
    * the name of a file for the output of the assembler
Use the out_type method to set up which output you want, e.g.:
You'll have to use the code in the bioperl-run subversion if you want to 
use these new features.



Paolo Pavan wrote:
> Dear,
> I'm confused about the proper usage of the module Bio::Tools::Run::Cap3.
> As documented in the pod, the run(@seqs) method returns the cap3 report file
> while I expect to return a Bio::Assembly object, consistently with other
> Bio::Tools::Run classes.
> However, I went around this by getting from the factory object the location
> and the names of the temp output files (actually accessing a private
> property, although) and reading them via the Assembly::IO system.
> I was just wandering what is the proper designed way to do this job.
> Thank you for enlighten the way!
> Paolo
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