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

Tue May 20 21:26:22 UTC 2014

Hi all,

maybe not the best moment, as you are busy releasing the new version:  
just wanted to inform you that the Bio.Phenotype module now supports  
sigmoid curve fitting and parameters extraction, only if scipy is  
installed.

The latest commits are here:  
https://github.com/mgalardini/biopython/tree/phenomics

The tests are working for either python2 and python3.

Hope this is of interesting,
Marco

----- Messaggio da marco.galardini at unifi.it ---------
     Data: Wed, 16 Apr 2014 19:11:25 +0200
       Da: Marco Galardini <marco.galardini at unifi.it>
Rispondi-A:Marco Galardini <marco.galardini at unifi.it>
  Oggetto: Re: [Biopython-dev] Interested in a Phenotype Microarray parser?
        A: Marco Galardini <marco.galardini at unifi.it>
       Cc: Peter Cock <p.j.a.cock at googlemail.com>, Biopython-Dev  
Mailing List <biopython-dev at lists.open-bio.org>

> Hi,
>
> regarding further additions to the Bio.Phenotype module I was
> considering the following solution to add support for sigmoid curve
> fitting and parameters extraction (which is of interest when analysing
> this kind of data). Since the easiest way to do the curve fitting is by
> using the scipy package, a solution may be to implement it as a
> "optional" feature, like the ability to draw trees with the Phylo
> module using matplotlib. An exception would be raised if the "function"
> is called with no scipy installed.
>
> Would it that be ok? Alternatively some other way to perform curve
> fitting may be found, but the maintenance may become very difficult.
>
> Marco
>
> ----- Messaggio da marco.galardini at unifi.it ---------
>     Data: Tue, 01 Apr 2014 00:59:32 +0100
>       Da: Marco Galardini <marco.galardini at unifi.it>
> Rispondi-A:Marco Galardini <marco.galardini at unifi.it>
>  Oggetto: Re: [Biopython-dev] Interested in a Phenotype Microarray parser?
>        A: Peter Cock <p.j.a.cock at googlemail.com>
>       Cc: Biopython-Dev Mailing List <biopython-dev at lists.open-bio.org>
>
>
>> 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
>> -------------------------------------------------
>>
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>
> ----- Fine del messaggio da marco.galardini at unifi.it -----
>
>
>
> Marco Galardini
> Postdoctoral Fellow
> EMBL-EBI - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD, UK
> Phone: +44 (0)1223 49 2547

----- Fine del messaggio da marco.galardini at unifi.it -----

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