[Bioperl-l] 1.01

[Lincoln Stein]

This is a little bit of a side-issue, but I would like to see the API
for retrieving a stream of analytic sequence features be the same as
the API for retrieving a stream of features from a database.  In both
cases, you pass the stream constructor a series of factory-specific
arguments, and retrieve a series of sequence features using
next_feature().  

I'm not sure how this relates to the next_seq() API used in SeqIO.

Lincoln


Catherine Letondal writes:
 > 
 > Jason Stajich wrote:
 > >Some projects on the table that one might hope would be part of 1.2:
 > >[...]
 > > * Design the interface based on the Bioperl/PISE to describe
 > >   remote analysis queues and add those classes to the main trunk.  Use
 > >   this interface for local execution as well as remote.
 > 
 > Hi,
 > 
 > Is it time to start discussions? I don't know exactly what questions are to be discussed 
 > yet? Anyway, these are my questions and suggestions ...
 > 
 > 1) creating the factory and running:
 > 
 >   # a) analysis queue (returns a Bio::Factory::Pise)
 >   $factory = new Bio::Factory::EMBOSS;
 >   # or:
 >   $factory = new Bio::Factory::Pise;
 > 
 >   # b) analysis application object (returns a Bio::Tools::Run::PiseApplication or
 >   # Bio::Tools::Run::EMBOSSApplication)
 >   $mfold = $factory->program('mfold');	
 > 
 >   # c) analysis results 
 >   $result = $mfold->run(); 		
 > 
 > 
 >   ... is that OK for EMBOSS and openBSA?
 > 
 >  
 > 2) general execution parameters:
 > 
 >  a) local or remote execution
 > 	- default could be local for EMBOSS and remote for Pise?
 > 	- in Pise, the default remote server could be different for different programs (I
 > 	mean, not only at Pasteur...:-) )
 > 
 >     - so one should be able to choose between local/remote execution and, if remote, to 
 >    choose a non-default server location; this choices could happen either at 
 >    factory creation, or at application creation, or at run step:
 > 	# a) at factory creation
 > 	$factory = new Bio::Factory::Pise(-remote => 'http://somewhere/cgi-bin/Pise');
 > 
 > 	# b) at application creation - take the default remote server
 > 	$needle = $factory->program('needle', -remote => 1);	
 > 
 > 	# c) at run time
 > 	$result = $mfold->run(-remote => 'http://bioweb.pasteur.fr/cgi-bin/seqanal/mfold.pl'); 
 > 
 > 
 >  b) email could be specified once at factory creation (for Pise)
 > 
 > 
 > 3) parameters specification
 > 
 >    a) when?  
 > 	# at factory creation?
 > 	$water = $factory->program('water', sequencea => $seqa,  seqall => $seqb);
 > 	$result1 = $water->run();
 > 
 > 	# before running?
 > 	$water->sequencea($seqc);
 > 	$result2 = $water->run();
 > 
 > 	# when running?
 > 	$result3 = $water->run(sequencea => $seqd);
 > 
 >    b) how?  -name or name
 > 
 > 
 > 4) analysis results: what is it, a string, an object, ...?
 > 
 >   $result = $fasta->run(); 
 > 		
 > 	- in Pise/bioperl $result is an instance of PiseJob, i.e a kind of "handle" from 
 >         which you can fetch results (image files, treefile, ...)
 > 	print $result->content("treefile");
 > 	print $result->stdout;
 > 	$result->save("blast2.txt");
 > 	etc...
 > 
 > 	- in Bio::Tools::Run::EMBOSSApplication, it's a string (the actual result): don't
 > 	you think it's more general to have an object?
 > 
 > 5) use of analysis result:
 > 
 >    - it's convenient to be able to build a handle from a result, in order
 >    to feed it to bioperl parsers or to other programs
 > 
 >     $aln = Bio::AlignIO->newFh (-fh => $needle_result->fh("outfile.align"), 
 >                                 -format => "fasta");
 >     $neighbor = $factory->program('neighbor', infile => $protdist_job->fh('outfile'));
 > 
 >    - construct an analysis result from an ID:
 >     $neighbor = $factory->result('http://bioweb.pasteur.fr/seqanal/tmp/blast2/A12465102130064/')
 > 
 > 6) misc:
 > 
 >  - It should be possible to issue an asynchronous run request (to enable parallel
 >    execution for long jobs)
 > 
 > 
 > How is all that compatible with OpenBSA?
 > 
 > --
 > Catherine Letondal -- Pasteur Institute Computing Center
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 > Bioperl-l mailing list
 > Bioperl-l@bioperl.org
 > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================