[Bioperl-l] BioPerl 1.6.901 and prot4est

[Fields, Christopher J]

Horácio,

Re: where the bug lies, it's hard to say.  There have been several significant changes with bioperl's Taxonomy/Tree code over the last several years.  Does the prot4est author (James Wasmuth) know about this?  

   http://www.compsysbio.org/lab/?q=prot4EST

You are also more than welcome to submit a bug report on this so we can track it.  The following page describes how and where to do so:

   http://www.bioperl.org/wiki/Bugs

(if you hear anything from the prot4est folks let us know)

chris

On May 21, 2012, at 12:28 PM, Horácio Montenegro wrote:

>    Dear all,
> 
>   I am trying to set up prot4est and ran into problems with the
> bioperl from debian testing repositories (1.6.901). It breaks one of
> the scripts (contructSMAT.pl) from prot4est:
> 
> ~/bin/p4e3.1b/exampleData$ ../bin/constructSMAT.pl --access
> p4e_access.txt --config ALC_smat.config
> CLEAN => 1
> SPECIES => Ascaris lumbricoides
> FSA_FILE => ~/bin/p4e3.1b/exampleData/./A.lumbricoides_sim.fsa
> EMBL_SEARCH => 1
> This dataset is from Ascaris lumbricoides (6252)
> Can't call method "ancestor" on an undefined value at
> /usr/local/share/perl/5.12.4/Bio/Taxon.pm line 513, <GEN0> line 1.
> 
>    The culprit is sub ancestor at Taxon.pm. Debugging a bit I found
> that a call to write_seq($emblO) on sub fsa2embl (from emblConnect.pl,
> another prot4est script) fires the bug. Anyway, the workaround so far
> is to use bioperl 1.6.1. In fact, if I use bioperl 1.6.901, but
> manually replace sub ancestor with the one from bioperl 1.6.1,
> prot4est runs normally.
> 
>   I do not know if this is a new bioperl bug, or if the changes in
> sub ancestor revealed some bug in emblConnect.pl.
> 
>    best regards,
>          Horacio
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