[ensembl-dev] get_SimpleAlign problem with cdna

Matthieu Muffato muffato at ebi.ac.uk
Wed Aug 15 16:32:09 BST 2012


Hi Sébastien

I have also just noticed this warning too. You can ignore it: the 
alignment is still correct.

I have patched the HEAD and branch-68 files on the CVS. You can update 
ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm and the 
script should not display that warning any more.

Regards,
Matthieu

On 15/08/12 16:16, Moretti Sébastien wrote:
> 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
>





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