[Biopython-dev] Interested in a Phenotype Microarray parser?
Peter Cock
p.j.a.cock at googlemail.com
Thu Aug 20 10:12:42 UTC 2015
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
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