[Biopython-dev] Interested in a Phenotype Microarray parser?

[Marco Galardini]

Hi,

many thanks for your comments, below some replies:

----- Messaggio da p.j.a.cock at googlemail.com ---------
     Data: Wed, 26 Mar 2014 10:14:53 +0000
       Da: Peter Cock <p.j.a.cock at googlemail.com>
Rispondi-A:Peter Cock <p.j.a.cock at googlemail.com>
  Oggetto: Re: [Biopython-dev] Interested in a Phenotype Microarray parser?
        A: Marco Galardini <marco.galardini at unifi.it>
       Cc: Biopython-Dev Mailing List <biopython-dev at lists.open-bio.org>


> On Tue, Mar 25, 2014 at 11:40 PM, Marco Galardini
> <marco.galardini at unifi.it> wrote:
>> Hi all,
>>
>> following your suggestions (as well as the other modules implementations)
>> I've just committed a couple of commits to my biopython fork, featuring the
>> Bio.Phenomics module.
>> The module capabilities are limited to reading/writing Phenotype Microarray
>> files and basic operations on the PlateRecord/WellRecord objects. The module
>> requires numpy to interpolate the signal when the user request a time point
>> that wasn't in the input file (this way the WellRecord object can be queried
>> with slices).
>> I'm thinking on how to implement the parameters extraction from WellRecord
>> objects without the use of scipy.
>>
>> Here's the link to my branch:
>> https://github.com/mgalardini/biopython/tree/phenomics
>> The module and functions have been documented taking inspiration from the
>> other modules: hope they are clear enough for you to try it out.
>> Some example files can be found in Tests/Phenomics.
>>
>> Marco
>
> Hi Marco,
>
> I've not worked with kind of data so my comments are not on
> the application specifics. But I'm pleased to see unit tests :)
>
> One thought was while you define (Java like?) getRow and getColumn
> methods, your __getitem__ does not support (NumPy like) access,
> which is something we do for multiple sequence alignments. I guess
> while most plates are laid out in a grid, the row/column for each
> sample is not the most important thing - the sample identifier is?
>
> Thinking out loud, would properties `rows` and `columns` etc be
> nicer than `getRow` and `getColumn`, supporting iteration over
> the rows/columns/etc and indexing?

Yeah, absolutely: I'll work on some changes to have a more  
straightforward way to select multiple WellRecords on row/column basis.

>
> Minor: Your longer function docstrings do not follow PEP257,
> specifically starting with a one line summary, then a blank line,
> then the details. Also you are using triple single-quotes, rather
> than triple double-quotes (like the rest of Biopthon).
> http://legacy.python.org/dev/peps/pep-0257/

Whoops, I'll change it, thanks

>
> Peter
>
> P.S. Also, I'm not very keen on the module name, phenomics -
> I wonder if it would earn Biopython a badomics award? ;)
> http://dx.doi.org/10.1186/2047-217X-1-6

That's meta-omics right? :p
What about 'Phenotype' then? Maybe it's too general, but future  
extensions may include other phenotypic readouts.

Marco
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----- Fine del messaggio da p.j.a.cock at googlemail.com -----



Marco Galardini
Postdoctoral Fellow
EMBL-EBI - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 49 2547