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

Michiel de Hoon mjldehoon at yahoo.com
Thu Aug 20 01:10:48 UTC 2015


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



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