[Bioperl-l] Bio::Tools::Run::Cap3 usage question
florent.angly at gmail.com
Tue Nov 24 17:54:48 EST 2009
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
* 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:
> 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!
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