[ensembl-dev] Inconsistent get_SimpleAlign behaviour ?

[Sébastien Moretti]

Hi

I use get_SimpleAlign function to get multiple sequence alignment from a 
gene tree object (e.g. ENSGT00390000003721)

Most of the time get_SimpleAlign returns the sequence with a short fasta 
header i.e. only the protein identifier.
This is what I expect (is expected ?).


Sometimes, the behaviour of get_SimpleAlign is inconsistent, it returns 
the protein identifier AND some sequence length information:
e.g.  ENSCJAP00000009838/1-575

It should return ENSCJAP00000009838 only.



I have seen that for several families like ENSGT00390000003721.
Do you see something similar ?

I don't know if the inconsistency comes from the ensembl API or from the 
BioPerl API I use to write the fasta file.

Regards

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