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

[Marco Galardini]

Hi,

as suggested, I've made a few changes to the proposed Bio.Phenotype 
module (apart from the less-omics name).

The PlateRecord object now can be indexed in a similar fashion as 
AlignIO multiple alignments: it is still possible to use the WellRecord 
identifier as an index, but when integers or slices are used, new 
sub-plates or single wells are returned. The system uses the well 
identifier as a mean to divide the plate into rows/column. Thanks for 
pointing out the AlignIO system, it has been very useful.
I've left the two getColumns and getRows functions, since for some 
people it may still be useful to use the wells identifiers. If you feel 
like they are too confusing I can remove them.

The updated branch is here: 
https://github.com/mgalardini/biopython/tree/phenomics

Kind regards,
Marco


On 26/03/2014 13:26, Marco Galardini wrote:
> 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
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>>
>
>
> ----- 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
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev

-- 
-------------------------------------------------
Marco Galardini, PhD
Dipartimento di Biologia
Via Madonna del Piano, 6 - 50019 Sesto Fiorentino (FI)

e-mail: marco.galardini at unifi.it
www: http://www.unifi.it/dblage/CMpro-v-p-51.html
phone:  +39 055 4574737
mobile: +39 340 2808041
-------------------------------------------------