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Bio::Tools::Run::AnalyUser3Contributed Perl DocumeBio::Tools::Run::Analysis(3)

NAME
       Bio::Tools::Run::Analysis - Module representing any (remote or local)
       analysis tool

SYNOPSIS
	 # run analysis 'seqret' using a default location and a default
	 # access method (which means using a Web Service at EBI)
	 use Bio::Tools::Run::Analysis;
	 print new Bio::Tools::Run::Analysis (-name => 'edit::seqret')
	      ->wait_for ({ sequence_direct_data => 'tatatacgtatacga',
			    osformat => 'embl'
			    })
	      ->result ('outseq');

	 # run a longer job without waiting for its completion
	 use Bio::Tools::Run::Analysis;
	 my $job = Bio::Tools::Run::Analysis->new(-name => 'edit::seqret')
			->run ({ sequence_direct_data => 'tatatacgtatacga',
				 osformat => 'embl'
				 });
	 # ...and after a while
	 $job->result ('outseq');

	 # get all results in the same invocation (as a hash reference
	 # with result names as keys) - let the module decide which
	 # results are binary (images in this examples) and save those
	 # in file (or files); it also shows how to tell that the module
	 # should read input data from a local file first
	 use Bio::Tools::Run::Analysis;
	 my $results =
	   Bio::Tools::Run::Analysis->new(-name => 'alignment_multiple::prettyplot')
	      ->wait_for ( { msf_direct_data => '@/home/testdata/my.seq' } )
	      ->results ('?');
	 use Data::Dumper;
	 print Dumper ($results);

	 # get names, types of all inputs and results,
	 # get short and detailed (in XML) service description
	 use Bio::Tools::Run::Analysis;
	 my $service = Bio::Tools::Run::Analysis->new(-name => 'edit::seqret');
	 my $hash1 = $service->input_spec;
	 my $hash2 = $service->result_spec;
	 my $hash3 = $service->analysis_spec;
	 my $xml = $service->describe;

	 # get current job status
	 use Bio::Tools::Run::Analysis;
	 print new Bio::Tools::Run::Analysis (-name => 'edit::seqret')
	   ->run ( { #...input data...
		   } )
	   ->status;

	 # run a job and print its job ID, keep the job un-destroyed
	 use Bio::Tools::Run::Analysis;
	 my $job =
	   Bio::Tools::Run::Analysis->new(-name => 'edit::seqret',
					  -destroy_on_exit => 0)
	   ->run ( { sequence_direct_data => '@/home/testdata/mzef.seq' } );
	 print $job->id . "\n";
	 # ...it prints (for example):
	 #    edit::seqret/c8ef56:ef535489ac:-7ff4

	 # ...in another time, on another planet, you may say
	 use Bio::Tools::Run::Analysis;
	 my $job =
	   Bio::Tools::Run::Analysis::Job->new(-name => 'edit::seqret',
					       -id => 'edit::seqret/c8ef56:ef535489ac:-7ff4');
	 print join ("\n",
		   $job->status,
		   'Finished: ' . $job->ended (1),   # (1) means 'formatted'
		   'Elapsed time: ' . $job->elapsed,
		   $job->last_event,
		   $job->result ('outseq')
		   );

	 # ...or you may achieve the same keeping module
	 # Bio::Tools::Run::Analysis::Job invisible
	 use Bio::Tools::Run::Analysis;
	 my $job =
	   Bio::Tools::Run::Analysis->new(-name => 'edit::seqret')
	       ->create_job ('edit::seqret/c8ef56:ef535489ac:-7ff4');
	 print join ("\n",
		   $job->status,
		   # ...
		   );

	 # ...and later you may free this job resources
	 $job->remove;

	 #
	 # --- See DESCRIPTION for using generator 'applmaker.pl':
	 #

DESCRIPTION
       The module represents an access to the local and/or remote analysis
       tools in a unified way that allows adding new access methods
       (protocols) seamlessly.

       At the moment of writing, there is available a SOAP access to almost
       all EMBOSS applications, running at the European Bioinformatics
       Institute.

       The documentation of all "public" methods are to be found in
       "Bio::AnalysisI". A tutorial (and examples how to call almost all
       public methods) is in the script "panalysis.PLS" (go to the "scripts"
       directory and type "perldoc panalysis.PLS").

       The module "Bio::Tools::Run::Analysis" uses general approach allowing
       to set arbitrary input data and to retrieve results by naming them.
       However, sometimes is more convenient to use a specific module,
       representing one analysis tool, that already knows about available
       input and result names. Such analyses-specific Perl modules can be
       generated by "papplmaker.PLS" generator. Its features and usage are
       documented in the generator (go to the "scripts" directory and type
       "perldoc papplmaker.PLS").

	 # this will generate module Seqret.pm
	 perl papplmaker.PLS -n edit.seqret -m Seqret

	 # ...which can be used with data-specific methods
	 use Seqret;
	 my $outseq = new Seqret
	   ->sequence_direct_data ('@/home/testdata/my.seq')
	   ->osformat ('embl')
	   ->wait_for
	   ->outseq
	   ;
	 print $outseq;

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   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
       Martin Senger (martin.senger@gmail.com)

COPYRIGHT
       Copyright (c) 2003, Martin Senger and EMBL-EBI.	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
       ยท   http://www.ebi.ac.uk/soaplab/Perl_Client.html

APPENDIX
       Here is the rest of the object methods.	Internal methods are preceded
       with an underscore _.

   new
	Usage	: my $tool =
		    Bio::Tools::Run::Analysis->new(-access => 'soap',
						   -name => 'edit.seqret',
						   ...
						   );
	Returns : a new Bio::Tools::Run::Analysis object representing the given tool
	Args	: There may be additional arguments which are specific
		  to the access method (see methods 'new' or '_initialize'
		  of the access-specific implementations (such as module
		  Bio::Tools::Run::Analysis::soap for a SOAP-based access).

		  The recognised and used arguments are:
		    -access
		    -location
		    -name
		    -httpproxy
		    -timeout

       It builds, populates and returns a new "Bio::Tools::Run::Analysis"
       object. This is how it is seen from the outside. But in fact, it
       builds, populates and returns a more specific lower-level object, for
       example "Bio::Tools::Run::Analysis::soap" object - which one it depends
       on the "-access" parameter.

       -access
	   It indicates what lower-level module to load.  Default is 'soap'.
	   Other (but future) possibilities may be:

	      -access => 'novella'
	      -access => 'local'

       -location
	   A location of the service. The contents is access-specific (see
	   details in the lower-level implementation modules).

	   Default is "http://www.ebi.ac.uk/soaplab/services" ( services
	   running at European Bioinformatics Institute on top of most of
	   EMBOSS analyses, and on few others).

       -name
	   A name of an analysis tool, or a name of its higher-level
	   abstraction, possibly including a category where the analysis
	   belong to. There is no default value (which usually means that this
	   parameter is mandatory unless your -location parameter includes
	   also the name (but it is then access-dependent).

       -destroy_on_exit => '0'
	   Default value is '1' which means that all
	   Bio::Tools::Run::Analysis::Job objects - when being finalised -
	   will send a request to the remote site to forget the results of
	   these jobs.

	   If you change it to '0' make sure that you know the job
	   identification - otherwise you will not be able to re-established
	   connection with it (later, when you use your program again). This
	   can be done by calling method "id" on the job object (such object
	   is returned by any of these methods: "create_job", "run",
	   "wait_for").

       -httpproxy
	   In addition to the location parameter, you may need to specify also
	   a location/URL of an HTTP proxy server (if your site requires one).
	   The expected format is "http://server:port".	 There is no default
	   value. It is also an access-specific parameter which may not be
	   used by all access methods.

       -timeout
	   For long(er) running jobs the HTTP connection may be time-outed. In
	   order to avoid it (or, vice-versa, to call timeout sooner) you may
	   specify "timeout" with the number of seconds the connection will be
	   kept alive. Zero means to keep it alive forever. The default value
	   is two minutes.

   VERSION and Revision
	Usage	: print $Bio::Tools::Run::Analysis::VERSION;
		  print $Bio::Tools::Run::Analysis::Revision;

Module Bio::Tools::Run::Analysis::Job
       It represents a job, a single execution of an analysis tool. Usually
       you do not instantiate these objects - they are returned by methods
       "create_job", "run", and "wait_for" of "Bio::Tools::Run::Analysis"
       object.

       However, if you wish to re-create a job you need to know its ID (method
       "id" gives it to you). The ID can be passed directly to the "new"
       method, or again you may use "create_job" of a
       "Bio::Tools::Run::Analysis" object with the ID as parameter. See
       SYNOPSIS above for an example.

       Remember that all public methods of this module are described in
       details in interface module "Bio::AnalysisI" and in the tutorial in the
       "analysis.pl" script.

   new
	Usage	: my $job = Bio::Tools::Run::Analysis::Job->new
			      (-access => 'soap',
			       -name => 'edit.seqret',
			       -id => 'xxxyyy111222333'
			       );
	Returns : a re-created object representing a job
	Args	: The same arguments as for Bio::Tools::Run::Analysis object:
		    -access
		    -location
		    -name
		    -httpproxy
		    -timeout
		    (and perhaps others)
		  Additionally and specifically for this object:
		    -id
		    -analysis

       -id A job ID created some previous time and now used to re-create the
	   same job (in order to re-gain access to this job results, for
	   example).

       -analysis
	   A "Bio::Tools::Run::Analysis" object whose properties (such as
	   "-access" and "-location" are used to re-create this job object.

Module Bio::Tools::Run::Analysis::Utils
       It contains several general utilities. These are "functions", not
       methods. Therefore call them like, for example:

	   &Bio::Tools::Run::Analysis::Utils::format_time (...);

   format_time
	Usage	: Bio::Tools::Run::Analysis::Utils::format_time ($time);
	Returns : Slightly formatted $time
	Args	: $time is number of seconds from the beginning of Epoch

       It returns what "localtime" returns which means that return value is
       different in the array and scalar context (see localtime). If $time is
       ``-1'' it returns 'n/a' (in the scalar context) or an empty array (in
       the array context). If $time is too small to represent the distance
       from the beginning of the Epoch, it returns it unchanged (the same in
       any contex) - this is reasonable for $time representing an elapsed
       time.

       The function is used to format times coming back from various job time
       methods.

   _load_access_module
	Usage	: $class->_load_access_module ($access)
	Returns : 1 on success, undef on failure
	Args	: 'access' should contain the last part of the
		  name of a module who does the real implementation

       It does (in the run-time) a similar thing as

	  require Bio::Tools::Run::Analysis::$access

       It prints an error on STDERR if it fails to find and load the module
       (for example, because of the compilation errors in the module).

   _guess_access
	Usage	: Bio::Tools::Run::Analysis::Utils::guess_access ($rh_params)
	Returns : string with a guessed access protocol (e.g. 'soap'),
		  or undef if the guessing failed
	Args	: 'rh_params' is a hash reference containing parameters given
		  to the 'new' method.

       It makes an expert guess what kind of access/transport protocol should
       be used to access the underlying analysis. The guess is based on the
       parameters in rh_params. Rememeber that this method is called only if
       there was no -access parameter which could tell directly what access
       method to use.

perl v5.14.1			  2011-07-21	  Bio::Tools::Run::Analysis(3)
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