[ensembl-dev] get_SimpleAlign problem with cdna

Moretti Sébastien sebastien.moretti at unil.ch
Wed Aug 15 16:16:40 BST 2012


Hi

I have a GeneTree object (-tree_type => 'tree', -member_type => 
'protein') and want to extract alignments from it.

No problem for protein alignment with
     $tree->get_SimpleAlign;


But it returns strange warnings, since I use API 68, for cdna:
     $tree->get_SimpleAlign(-cdna=>1);

Use of uninitialized value $id_type in string eq at
 
/usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMemberSet.pm 
line 265 (#1)
     (W uninitialized) An undefined value was used as if it were already
     defined.  It was interpreted as a "" or a 0, but maybe it was a 
mistake.
     To suppress this warning assign a defined value to your variables.

     To help you figure out what was undefined, perl will try to tell 
you the
     name of the variable (if any) that was undefined. In some cases it 
cannot
     do this, so it also tells you what operation you used the undefined 
value
     in.  Note, however, that perl optimizes your program and the operation
     displayed in the warning may not necessarily appear literally in your
     program.  For example, "that $foo" is usually optimized into "that "
     . $foo, and the warning will refer to the concatenation (.) operator,
     even though there is no . in your program.

Use of uninitialized value $id_type in string eq at
 
/usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMemberSet.pm 
line 266 (#1)



Any idea of what happens there ?
Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/




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