[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
modifications
Just to give two examples: according to the documentation on
http://www.ensembl.org/info/docs/Pdoc/ensembl-compara/index.html
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
questions.
Many thanks,
Lel
_____________________________________________________________________
Lel Eory
Institute of Evolutionary Biology
The University of Edinburgh
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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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