/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::PiseJob

NAME

Bio::Tools::Run::PiseJob - A class to manage Pise 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");

my $job = $program->run(-seq => $ARGV[0]);

# 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::PiseJob class handles a specific job state and results. A Bio::Tools::Run::PiseJob instance should be created by a subclass of Bio::Tools::Run::PiseApplication class, e.g Bio::Tools::Run::PiseApplication::genscan or Bio::Tools::Run::PiseApplication::dnapars, ... (see Bio::Tools::Run::PiseApplication class) :

my $job = Bio::Tools::Run::PiseJob->new($self, $self->{VERBOSE});

This class may also be used as a mean to get informations about a running job, or to get results after a long computation:

my $job = Bio::Factory::Pise->job($url);
print $job->content('infile.aln');

Once the job is created, you can get results:

foreach my $result ($job->get_results) {
  print $job->content($result);
  $job->save($result, "myfile"); # $job->save($result) keeps the name
  print $job->stdout;            # print job standard output
  print $job->stderr;            # print job standard error
}

You can feed a result file as a filehandle to a bioperl parser :

my $parser = Bio::Tools:Genscan->new (-fh => $job->fh('genscan.out'));
my $parser = Bio::Tools:BPlite->new (-fh => $job->fh('blast2.txt'));

... or to another pise job:

  my $neighbor = $factory->program ('neighbor',
			            -infile => $job->fh('outfile'));

You can lookup up for a type of result that could be piped to another Pise program:

my $matrix = $job->lookup_piped_file('phylip_dist');

returns the url of the just calculated Phylip distances matrix file, produced by e.g DNADIST or PROTDIST.

All the available pipe types may be obtained by:

$job->lookup_piped_files;

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/wiki/Mailing_lists  - 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 the web:

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

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::PiseApplication

new

Title   : new()
Usage   : $job = Bio::Tools::Run::PiseJob->new($application, $verbose);
Function: Creates a Bio::Tools::Run::PiseJob object. 
          This is normally called by an application object
          - i.e a subclass of the Bio::Tools::Run::PiseApplication class, 
          for submitting a job. 
          This method actually submit the job and parse results.
Example :
Returns : An instance of Bio::Tools::Run::PiseJob.

verbose

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

job

Title   : job()
Usage   : $job = Bio::Tools::Run::PiseJob->job(url);
Function: Creates a Bio::Tools::Run::PiseJob object from an already 
          run job by giving the url of the job result page.
          May also be called through Bio::Factory::Pise->job(url);
Example :
Returns : An instance of Bio::Tools::Run::PiseJob.

jobid

Title   : jobid()
Usage   : $job->jobid();
Function: Returns the url of the job result page.
Example :
Returns :

error

Title   : error()
Usage   : $job->error();
Function: Tells if the job has been successfully run. This is the case 
          when the job has been submitted, but the Pise server has 
          detected user errors (missing mandatory parameter, unallowed 
          value,...). This also happen when the user provided an
          invalid url, or the http request could not be submitted.
          See method error_message().

Example :
Returns : TRUE/FALSE

error_message

Title   : error_message()
Usage   : $job->error_message();
Function: Returns the error message.
Example :
Returns : A string.

get_results

Title   : get_results()
Usage   : $job->get_results();
Function: Provides the urls of the result files.
Example :
Returns : A list of urls.

get_pipes

Title   : get_pipes()
Usage   : $job->get_pipes($result);
Function: Provides the names of the programs that can use this type of
          result. $result is an url, that can be provided through the
          get_results method.
Example :
Returns : A list of program names.

piped_file_type

Title   : piped_file_type()
Usage   : $job->piped_file_type($result);
Function: Provides the Pise type of $result. $result is an url, 
          that can be provided through the get_results method.
Example :
Returns : A Pise pipetype name.

lookup_piped_files

Title   : lookup_piped_files()
Usage   : $pipe_types = $job->lookup_piped_files();
Function: Returns the pipe types produced by the job
          (e.g:  phylip_tree, seqsfile, readseq_ok_alig, ...). 
          You have to call lookup_piped_file($type) to get the actual
          correponding result file.
Example :
Returns : A string.

lookup_piped_file

Title   : lookup_piped_file(type)
Usage   : $result = $job->lookup_piped_file($type);
Function: Returns the name of the result file of pipe type $type 
          (e.g:  phylip_tree, seqsfile, readseq_ok_alig, ...). $result 
          is an url.
Example :
Returns : A string (an url).

terminated

Title   : terminated()
Usage   : $job->terminated();
Function: Tells whether the job has terminated.
Example :
Returns : TRUE/FALSE.

save

Title   : save()
Usage   : $filename = $job->save($result);
          $filename = $job->save($result, $name);
Function: Save the result in a file. $result is an url, 
          that can be provided through the get_results method. You can
          provide your own filename. By default, the file name will be
          the same as the result name.
Example :
Returns : A file name.

content

Title   : content()
Usage   : $s = $job->content($result);
Function: Provides the content of $result. $result is an url, 
          that can be provided through the get_results method. 
          By default, $result is the standard output.
Example :
Returns : A string.

stdout

Title   : stdout()
Usage   : print $job->stdout();
Function: Provides the content of the job standard output. 
Example :
Returns : A string.

stderr

Title   : stderr()
Usage   : print $job->stderr();
Function: Provides the content of the job standard error. 
Example :
Returns : A string.

fh

 Title   : fh()
 Usage   : $fh = $job->fh($result);
 Function: Provides a filhandle for a result.
           $result is an url, that can be provided through the 
           get_results method. 

           Be aware that you must re-ask for it for a subsequent use. For
           instance, if you first use it for an input parameter:
             my $program = Pise::program->new ( ...,
		  			      file => $previous_job->fh('..'),
					      );
             my $job = $program->run;

           A subsequent run of the same object: will need a re-initialization:
             $program->file($previous_job->fh('..'));
             my $job2 = $program->run;

 Example :
 Returns : A filehandle.

results_type

Title   : results_type()
Usage   : $job->results_type($type);
Function: Enables to change result delivery from one email per file
          to url notification or attached files. $type is either: url, 
          attachment, email. 
Example :
Returns : 1 if success, 0 if job already terminated.

value

Title   : value(param)
Usage   : $job->value(param);
Function: 
Example :
Returns : value of parameter param, if available.

_init

Title   : _init()
Usage   : $self->_init;
Function: Internal. Initializes parameters. Called by new.
Example :
Returns :

_submit

Title   : _submit()
Usage   : $self->_submit();
Function: Internal. Sends the http request on a Pise server. Called by new.
Example :
Returns : -1 if an error has occured
          jobid else
Exceptions: when the job has already been submitted.

_parse

Title   : _parse()
Usage   : $self->_parse();
Function: Internal. Parses Pise XHTML results page and fills data structures.
          Called by frmoUrl or by _submit.
Example :
Returns :

READLINE

Title   : READLINE()
Usage   : 
Function: Internal - see perltie.
Example :
Returns : A string.

TIEHANDLE

Title   : TIEHANDLE()
Usage   : 
Function: Internal - see perltie.
Example :
Returns :

CLOSE()

Title   : CLOSE()
Usage   : 
Function: Internal - see perltie.
Example :
Returns :

_clean_content

Title   : _clean_content()
Usage   : my $content = $self->_clean_content($content);
Function: Internal. Useful to call before XML parsing.
Example :
Returns :