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

Paolo Pavan paolo.pavan at gmail.com
Tue Nov 24 14:28:09 EST 2009

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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