[Bioperl-l] BioPerl 1.6.901 and prot4est

[Horácio Montenegro]

    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