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

[Peter Cock]

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?

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/

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