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 / 
bioperl-run-1.4
/ Bio::Tools::Run::PiseApplication

NAME

Bio::Tools::Run::PiseApplication - A class manage Pise programs information, configuring parameters and submit jobs.

SYNOPSIS

  use Bio::Tools::Run::AnalysisFactory::Pise;

  # Build a Pise factory       
  my $factory = new Bio::Tools::Run::AnalysisFactory::Pise();

  # Then create an application object (Pise::Run::Tools::PiseApplication):
  my $program = $factory->program('genscan');

  # Set parameters
  $program->seq($ARGV[0]);

  # Next, run the program
  # (notice that you can set some parameters at run time)
  my $job = $program->run(-parameter_file => "Arabidopsis.smat");

  # Test for submission errors:
  if ($job->error) {
     print "Job submission error (",$job->jobid,"):\n";
     print $job->error_message,"\n";
     exit;
  }

  # Get results
  print STDERR $job->content('genscan.out');
  # or:
  my $result_file = $job->save('genscan.out');

DESCRIPTION

A class to manage Pise programs information, configuring parameters and submit jobs. It is the super-class of all the Bio::Tools::Run::PiseApplication::program classes.

This class is preferably created through the Bio::Tools::Run::AnalysisFactory::Pise factory:

  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
  my $program = $factory->program('mfold');

By submitting a job, you create a Bio::Tools::Run::PiseJob instance with the parameters you have just set. Bio::Tools::Run::PiseJob class handles a specific job state and results.

  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                          -email => 'me@myhome');
  my $program = $factory->program('water', 
                                    -sequencea => $seqa,
                                    -seqall => $seqb);

  # run: submit and waits for completion
  my $job = $program->run();

  # for long jobs
  my $job = $program->submit(); # only submit the request
  my $jobid = $job->jobid;
  # later, from another script
  my $job = Bio::Tools::Run::PiseJob->fromUrl($jobid);
  if ($job->terminated) {
      print $job->stdout;
  }

Pise parameters setting.

The @params list should contain a list of -parameter => value pairs.

  my @params = (-query => $file, -protein_db => "genpept");
  my $program = $factory->program('blast2', @params);

or directly :

  my $program = $factory->program('blast2', query => $file, protein_db => "genpept");

Each program parameter is described in the documentation of the corresponding Bio::Tools::Run::PiseApplication::program documentation.

You can change parameters at any time by calling the corresponding method, e.g, changing the parameter E in blast2:

  my $program = $factory->program('blast2', -protein_db => "genpept");
  $program->query($seq);
  $program->Expect($value);

Parameter of Pise type "Sequence" and "InFile" may be given as string, filename, or filehandle. Parameter of type "Sequence" may also be given as Bio::Seq or Bio::SimpleAlign objects.

Job output

See Bio::Tools::Run::PiseJob for how to fetch results and chain programs.

Location and email parameters

Email can be set at factory creation.

The location parameter stands for the actual CGI location. There are default values for most of Pise programs.

You can either set location at:

1 factory creation
  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                 -location = 'http://somewhere/Pise/cgi-bin',
                                 -email => 'me@myhome');
2 program creation
  my $program = $factory->program('water', 
                    -location = 'http://somewhere/Pise/cgi-bin/water.pl'
                                  );
3 any time before running:
  $program->location('http://somewhere/Pise/cgi-bin/water.pl');
  $program->run();
4 when running:
  $job = $program->run(-location => 'http://somewhere/Pise/cgi-bin/water.pl');

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $program = Bio::Tools::Run::PiseApplication->new($location, 
                                                               $email);
 Function: Creates a Bio::Tools::Run::PiseApplication::program object, 
           where program stands for any 
           of the Pise programs.
           This method should not be used directly, but rather by 
           a Bio::Tools::Run::AnalysisFactory::Pise instance.
 Example :
 Returns : An instance of Bio::Tools::Run::PiseApplication::program.

location

 Title   : location
 Usage   : my $location = $program->location;
 Function: Called from Bio::Tools::Run::PiseJob to get/set program/Pise 
           configuration informations from the 
           Bio::Tools::Run::PiseApplication::program class.
 Example :
 Returns : A string containing the url of the Pise server CGI.

email

 Title   : email()
 Usage   : my $email = $program->email();
 Function: Called from Bio::Tools::Run::PiseJob to get/set program/Pise 
           configuration informations from the 
           Bio::Tools::Run::PiseApplication::program class.
 Example :
 Returns : A string containing the user email for submissions.

verbose

 Title   : verbose()
 Usage   : $program->verbose(1);
 Function: Ask the object to tells more.
 Example :
 Returns : Actual value.

param_type

 Title   : param_type()
 Usage   : my $type = $program->param_type($param);
 Function: Tells the Pise parameter type of $param (e.g: Sequence, 
           String, Excl, ...).
 Example :
 Returns : A string containing the Pise parameter type.

run

 Title   : run()
 Usage   : $program->run();
           $program->run(10);
 Function: Submit the job and waits for completion. You may provide an
           interval for completion checking.
 Example :
 Returns : The instance of Bio::Tools::Run::Pisejob that has been run.

submit

 Title   : submit()
 Usage   : $program->submit();
 Function: Submit the job.
 Example :
 Returns : The instance of Bio::Tools::Run::Pisejob that has been run.

results_type

 Title   : results_type()
 Usage   : $program->results_type($type);
 Function: Enables to change result delivery from one email per file
           to url notification or attached files. $type is either: url, 
           attachment, email. This information will be provided to the job
           when detached and submitted through the run method.
 Example :
 Returns :

paraminfo

 Title   : paraminfo()
 Usage   : $program->paraminfo();
 Function: Displays parameters and prompts.
 Example :
 Returns :

_init_params

 Title   : _init_params
 Usage   : $self->_init_params(@params);
 Function: Internal. To be called from Pise::program::new method after
           all the data structures have been initialized.
 Example :
 Returns :

_OK_FIELD

 Title   : _OK_FIELD()
 Usage   : if ($self->_OK_FIELD($param)) ...
 Function: Checks if $param is a known parameter for the specific program.
 Example :
 Returns : TRUE/FALSE