[Biopython-dev] Interested in a Phenotype Microarray parser?
Marco Galardini
marco.galardini at unifi.it
Thu Aug 20 11:09:42 UTC 2015
Hi Peter,
I've updated the previous pull request:
https://github.com/biopython/biopython/pull/598
Thanks a lot for your support, please let me know if I can be of any
help in writing a small tutorial/documentation.
Best,
Marco
Il Giovedì 20/08/2015 12:12 Peter Cock ha scritto:
> Great. Marco, are you happy to make a pull request on GitHub?
>
> I'm willing to look over the code for general issues & merge it.
>
> Peter
>
> On Thu, Aug 20, 2015 at 2:10 AM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
>> Looks good to me. I think we should include it.
>> Best,
>> -Michiel.
>>
>> --------------------------------------------
>> On Wed, 8/19/15, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> Subject: Re: [Biopython-dev] Interested in a Phenotype Microarray
>> parser?
>> To: "Marco Galardini" <marco.galardini at unifi.it>, "Michiel de Hoon"
>> <mjldehoon at yahoo.com>
>> Cc: "Biopython-Dev Mailing List" <biopython-dev at lists.open-bio.org>
>> Date: Wednesday, August 19, 2015, 11:12 PM
>>
>> What do you think
>> Michiel? You're probably the most appropriate person
>> to look at this.
>>
>> (I've never used Phenotype Microarray
>> plates)
>>
>> Or anyone else?
>>
>> Peter
>>
>> On
>> Fri, Aug 14, 2015 at 3:13 PM, Marco Galardini
>> <marco.galardini at unifi.it>
>> wrote:
>> >
>> > 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
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
More information about the Biopython-dev
mailing list