[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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