[Biopython-dev] Interested in a Phenotype Microarray parser?
Marco Galardini
marco.galardini at unifi.it
Fri Aug 14 14:13:12 UTC 2015
Hi all,
I just realised that more than one year ago I made this pretty simple
Phenotype Microarray data parser for BioPython
(https://github.com/mgalardini/biopython/tree/phenomics).
Are you still interested in including it? In any case I was thinking of
releasing it as a stand-alone library.
Any suggestion or feedback is very welcome.
Best,
Marco
Il Martedì 20/05/2014 23:26 Marco Galardini ha scritto:
> 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
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