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Summary

Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise
application objects.

Package variables

Included modules

Inherit

Bio::Factory::ApplicationFactoryI Bio::Root::Root

Synopsis

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

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

  # 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

Bio::Tools::Run::AnalysisFactory::Pise is a class to create Pise
application objects, that let you submit jobs on a Pise server.

  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                              -email => 'me@myhome');

The email is optional (there is default one). It can be useful,
though. Your program might enter infinite loops, or just run many
jobs: the Pise server maintainer needs a contact (s/he could of course
cancel any requests from your address...). And if you plan to run a
lot of heavy jobs, or to do a course with many students, please ask
the maintainer before.
The location parameter stands for the actual CGI location, except when
set at the factory creation step, where it is rather the root of all
CGI. There are default values for most of Pise programs.
You can either set location at:
   
   
   
   
You can also retrieve a previous job results by providing its url:

  $job = $factory->job($url);

You get the url of a job by:

  $job->jobid;

Methods

Methods description

 Title   : new()
 Usage   : my $program = Bio::Tools::Run::AnalysisFactory::Pise->new(
                               -location => 'http://somewhere/cgi-bin/Pise', 
                               -email => $email);
 Function: Creates a Bio::Tools::Run::AnalysisFactory::Pise object, which 
           function is to create interface object 
           (Bio::Tools::Run::PiseApplication::program) for programs.
 Example :
 Returns : An instance of Bio::Tools::Run::AnalysisFactory::Pise.

 Title   : program()
 Usage   : my $program = Bio::Tools::Run::AnalysisFactory::Pise->program(
                             $program, 
                             -location => 'http://somewhere/cgi-bin/Pise',
                             -email => $email,
                             @params);
 Function: Creates a representation of a single Pise program.
 Example :
 Returns : An instance of Bio::Tools::Run::PiseApplication::$program.

 Title   : job(url)
 Usage   : my $job = Bio::Tools::Run::AnalysisFactory::Pise->job(
              'http://somewhere/cgi-bin/Pise/tmp/dnapars/A3459687595869098');
 Function: Creates a previously run job by providing its jobid (url of 
           results).
 Example :
 Returns : An instance of Bio::Tools::Run::PiseJob.

Methods code

sub new {

    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($location) =
	$self->_rearrange([qw(LOCATION )],
			  @args);
    my ($email) =
	$self->_rearrange([qw(EMAIL )],
			@args);
    
    my ($verbose) =
	$self->_rearrange([qw(VERBOSE )],
			  @args);
    
    if (defined $location) {
	$self->{LOCATION} = $location;
    }

    if (defined $email) {
	$self->{EMAIL} = $email;
    } else {
	$self->{EMAIL} = 'pise-bioapi@pasteur.fr';
    }
    if (defined $verbose) {
	$self->{VERBOSE} = $verbose;
    } else {
	$self->{VERBOSE} = 0;
    }
    return $self;

}

sub program {

    my ($self, $program, @args) = @_;

    my ($location) =
      $self->_rearrange([qw(LOCATION )],
			@args);
    my ($email) =
	$self->_rearrange([qw(EMAIL )],
			  @args);

    my ($verbose) =
	$self->_rearrange([qw(VERBOSE )],
			  @args);
    if (! $location) {
	if (defined $self->{LOCATION}) {
	    if ($self->{LOCATION} =~ /$program/) {
		$location = $self->{LOCATION};
	    } else {
		$location = $self->{LOCATION} . "/$program.pl";
	    }
	} else {
	    if (defined $LOCATION{$program}) {
		$location = $LOCATION{$program};
	    } else {
		$location = $LOCATION{'default'} . "/$program.pl";
	    }
	}
    }
    if (! $email) {
	$email = $self->{EMAIL};
    }
    if (! $verbose) {
	$verbose= $self->{VERBOSE};
    }

    no strict "subs";

    my $package = "Bio::Tools::Run::PiseApplication::$program";  
    my $pise_program;

    eval ("use $package");
    $self->throw("Problem to load Bio::Tools::Run::PiseApplication::${program}\n\n$@")
	if $@;

    eval($pise_program = $package->new($location, $email) );
    use strict "subs";

    foreach my $param ($pise_program->parameters_order) {
	my $param_name = $param;
	$param_name =~ tr/a-z/A-Z/;
	#print STDERR "setting $param_name ...?\n";
	my ($value) =
	    $self->_rearrange([$param_name],
			      @args);
	if ($value) {
	    #print STDERR "setting $param to $value\n";
	    $pise_program->$param($value);
	}
    }

    #print STDERR "creation of $pise_program ", ref($pise_program), "\n"; 
    return $pise_program;

}

sub job {

    my ($self, $jobid) = @_;
    my $job = Bio::Tools::Run::PiseJob->job($jobid);
    return $job;
}

1;

}

General documentation

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/wiki/Mailing_lists  - About the mailing lists

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 the
web:

  http://bugzilla.open-bio.org/

Catherine Letondal (letondal@pasteur.fr)

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.

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

Bio::Tools::Run::PiseApplication
Bio::Tools::Run::PiseJob