[ensembl-dev] update of module documentation

Lel Eory lel.eory at ed.ac.uk
Tue Oct 19 11:43:05 BST 2010

Hello there,

I wonder whether it would be possible to get the module documentations 
updated for the Perl API. I am working with the Compara module and 
although the implementations work very well I find it hard to identify 
the functions I need, because
1) many of the methods lack the description
2) the descriptions do not reflect the actual code due to subsequent 

Just to give two examples: according to the documentation on 
a) Homology objects has a method called "get_SimpleAlign" which returns 
either with amino-acid or cDNA alignments depending on an argument. For 
Family objects the same method is missing the description and although 
it accepts the argument 'cdna' it returns only with amino-acid 
alignments without warning.
b) for Attribute objects the method "cdna_alignment_string" has only one 
argument specified as 'none', but in reality it has two arguments the 
first is a Member object, while the second, I assume, is to define how 
to deal with selenocysteines.

Updating the documentations, especially the descriptions, would be 
immensely helpful and would save a lot of time for us who are using the 
Perl API to get access to the data stored by Ensembl, and it may also 
reduce the workload on those of you who provide the answers to our 

Many thanks,

  Lel Eory
  Institute of Evolutionary Biology
  The University of Edinburgh

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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