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

[Michiel de Hoon]

Hi Marco,

> will you be interested in the addition of a PM data files
> parser in Biopython? 
Yes it makes sense to me.

> any specification on the style guide for the biopython parsers?
There is no strict set of rules, but to get you started, many modules
follow this format:
- Assuming a PM data file contains only a single data set, the module
should contain a function "read" that takes either a file name or a file
handle as the argument.
- The module should contain a class (typically called "Record") that
can store the data in the data file. The "read" function returns an
object of this class.
- Try to avoid third-party dependencies if at all possible.

Would it make sense to have a single Bio.Microarray module that can
house the various microarray parsers (PM, Affy, others)?

Best,
-Michiel.



--------------------------------------------
On Tue, 1/7/14, Marco Galardini <marco.galardini at unifi.it> wrote:

 Subject: [Biopython-dev] Interested in a Phenotype Microarray parser?
 To: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
 Date: Tuesday, January 7, 2014, 8:51 AM
 
 Dear biopythoners,
 
 will you be interested in the addition of a PM data files
 parser in Biopython? Such phenotypic data should be widely
 used in microbial experiments, even though just a few
 tools/libraries are available to parse and analyze such data
 (so far it's available a R package called opm and a python
 command line tool developed by me, called DuctApe). If you
 think that the ability to parse such files and perform some
 basic analysis (like curve parameters extraction) would be
 interesting as a new feature for biopython, I would very
 much like to contribute.
 
 If you were interested in such addition, could you
 pleaseindicate if there is any specification on the style
 guide for the biopython parsers?
 
 Thanks for the amazing work,
 Marco
 
 -- -------------------------------------------------
 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
 -------------------------------------------------
 
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