Bio::Tools::Run::PiseJob - A class to manage Pise jobs.
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');
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;
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::AnalysisFactory::Pise Bio::Tools::Run::PiseApplication
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.
Title : verbose() Usage : $program->verbose(1); Function: Ask the object to tells more. Example : Returns :
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.
Title : jobid() Usage : $job->jobid(); Function: Returns the url of the job result page. Example : Returns :
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
Title : error_message() Usage : $job->error_message(); Function: Returns the error message. Example : Returns : A string.
Title : get_results() Usage : $job->get_results(); Function: Provides the urls of the result files. Example : Returns : A list of urls.
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.
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.
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.
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).
Title : terminated() Usage : $job->terminated(); Function: Tells whether the job has terminated. Example : Returns : TRUE/FALSE.
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.
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.
Title : stdout() Usage : print $job->stdout(); Function: Provides the content of the job standard output. Example : Returns : A string.
Title : stderr() Usage : print $job->stderr(); Function: Provides the content of the job standard error. Example : Returns : A string.
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.
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.
Title : value(param) Usage : $job->value(param); Function: Example : Returns : value of parameter param, if available.
Title : _init() Usage : $self->_init; Function: Internal. Initializes parameters. Called by new. Example : Returns :
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.
Title : _parse() Usage : $self->_parse(); Function: Internal. Parses Pise XHTML results page and fills data structures. Called by frmoUrl or by _submit. Example : Returns :
Title : READLINE() Usage : Function: Internal - see perltie. Example : Returns : A string.
Title : TIEHANDLE() Usage : Function: Internal - see perltie. Example : Returns :
Title : CLOSE() Usage : Function: Internal - see perltie. Example : Returns :
Title : _clean_content() Usage : my $content = $self->_clean_content($content); Function: Internal. Useful to call before XML parsing. Example : Returns :
To install Bio::Factory::EMBOSS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Factory::EMBOSS
CPAN shell
perl -MCPAN -e shell install Bio::Factory::EMBOSS
For more information on module installation, please visit the detailed CPAN module installation guide.