[ensembl-dev] Minor Improvements to VariationAdaptor.pm

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Tue Aug 24 22:05:03 BST 2010


Hi all,

I made a few minor improvements for VariationAdaptor.pm:

1. In both get_all_by_dbID_list and get_all_by_name_list methods, when
the query list is only 1 element in length, $id_str would be currently
set without single quotes around the query, which would cause mySQL to
mistoke that as a column name. I have added back the single quotes.

2. I have implemented the synonym table search in get_by_name in
get_all_by_name_list, but with a single issue: Any Variation objects
that are only found in this search would be put *before* those found in
the first search. 

Although I made basic tests on my system, I'm not savvy enough in this
stuff to be sure if that works right-- especially given I forgot what I
learnt in SQL. Comments are appreciated.

Cheers,

John MC Ma
Graduate Assistant
Kwitek Lab
Department of Internal Medicine
3125E MERF
375 Newton Road
Iowa City IA 52242
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