[BioPython] Pise client

[Catherine Letondal]

Hi,

I have written a Python package to run jobs on a Pise Web server from a python 
program (Pise is a tool to generate user interfaces for programs running under Unix
described here: http://www-alt.pasteur.fr/~letondal/Pise).

For example, the following script run a toppred job on a SeqRecord instance, displays
the standard output of this job, and save the graphical output in a file. Sequences 
or alignments can be input either as Seq, SeqRecord, files or just strings.

from Pise import PiseFactory
import Bio.Fasta
import sys

factory = PiseFactory(email='user@domain')
program = factory.program("toppred",
                          graph_output=1,
                          profile_format="ps")

handle = open(sys.argv[1])
it = Bio.Fasta.Iterator(handle, Bio.Fasta.SequenceParser())
seq = it.next()

job = program.run(query=seq)

if job.error():
      print job.error_message()
else:
      print "url of the job: " + job.jobid()
      print job.stdout()
      print "Results: ", job.get_results()
      job.save('.ps')


The package is available at: http://www-alt.pasteur.fr/~letondal/Pise/#pisepython

The package is organized in 4 main classes (the package is organized about the same 
way as in the bioperl API in fact):

       PiseFactory
       -----------
       builds PiseApplication
       instances
       program()
         |
         |
         v

       PiseApplication       PiseJob               PiseJobParser
       ---------------       -------               -------------
       object          -->   actual job            (an xml.sax.handler) to parse 
       to set                (methods to           XHTML server output
       parameters            actually submit  
       and launch            the http request
       jobs                  via httplib,
                             get job state
         |                   and results)
         |
       +----------------------------------------------+
       | toppred fasta hmmbuild nnssp blast2 clustalw |
       | genscan tacg dnapars wublast2 ...            |
       |                                              |
       +----------------------------------------------+


I'm aware about the Bio.Application framework, but I have understood it's more for local
run. For instance, AbstractCommandline would have been useful on a server, but
there is no such thing in the client, which does not deal with command lines.
It should be possible to wrap PiseApplication classes in Bio.Application classes though
(and ApplicationResult sub-class could re-use PiseJob methods for instance).


I have tried to put the minimum information in the numerous files that belongs to this
package (there is a small file for each program, and there are about 287 programs). 


I would be very happy to get some feedback about this code!


-- 
Catherine Letondal -- Pasteur Institute Computing Center