[ensembl-dev] Minor Improvements to VariationAdaptor.pm

[Will McLaren]

Hi John,

Thanks very much for looking into this! I will do some testing on your code,
then if it's OK with you I will add it to the repository and it will appear
in release 60.

Cheers,

Will McLaren
Ensembl Variation

On 24 August 2010 22:05, Ma, Man Chun John <manchunjohn-ma at uiowa.edu> wrote:

> 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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