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Bio::SimpleAnalysisI(3User Contributed Perl DocumentatiBio::SimpleAnalysisI(3)

       Bio::SimpleAnalysisI - A	simple interface to any	(local or remote)
       analysis	tool

       This is an interface module - you do not	instantiate it.	 Use other
       modules instead (those that implement this interface).

       This interface contains public methods for accessing and	controlling
       local and remote	analysis tools.	It is meant to be used on the client
       side. The interface consists only of a necessary	set of methods for
       synchronous invocation of analysis tools. For more complex set,
       including an asynchronous access, see interface "Bio::AnalysisI"	(which
       inherits	from this one, by the way).

   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.			- General discussion	- About	the mailing lists

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

       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

       Martin Senger (

       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.

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


       This is actually	the main documentation...

       If you try to call any of these methods directly	on this
       "Bio::SimpleAnalysisI" object you will get a not	implemented error

	Usage	: $tool->analysis_name;
	Returns	: a name of this analysis
	Args	: none

	Usage	: $tool->analysis_spec;
	Returns	: a hash reference describing this analysis
	Args	: none

       The returned hash reference uses	the following keys (not	all of them
       always present, perhaps others present as well):	"name",	"type",
       "version", "supplier", "installation", "description".

	Usage	: $tool->input_spec;
	Returns	: an array reference with hashes as elements
	Args	: none

       The analysis input data are named, and can be also associated with a
       default value, with allowed values and with few other attributes. The
       names are important for feeding the analysis with the input data	(the
       inputs are given	to methods "run" and "wait_for"	as name/value pairs).

	Usage	: $tool->result_spec;
	Returns	: a hash reference with	result names as	keys
		  and result types as values
	Args	: none

       An analysis can produce several results,	or the same result in several
       different formats. All such results are named and can be	retrieved
       using their names by metod "result".

       Here is an example of the result	specification:

	 $result_spec =	{
		 'outseq' => 'String',
		 'report' => 'String',
		 'detailed_status' => 'String'

	Usage	: $tool->run ( ['sequence=@my.seq', 'osformat=embl'] )
	Returns	: $self
	Args	: data and parameters for this execution
		  (in various formats)

       Create a	job, start it, and wait	for its	completion. The	method is
       identical to the	method "wait_for". Why there are two methods doing the
       same? Because it	is expected that the sub-classes may implement them
       differently (an example is an interface "Bio::AnalysisI"	which uses
       method "run" for	an asynchronous	execution and method "wait_for"	for a
       synchronous one.

       Usually,	after this call, you ask for results of	the finished job:

	   $analysis->run (...)->result;

       The input data and prameters for	this execution can be specified	in
       various ways:

       array reference
	   The array has scalar	elements of the	form

	      name = [[@]value]

	   where "name"	is the name of an input	data or	input parameter	(see
	   method "input_spec" for finding what	names are recognized by	this
	   analysis) and "value" is a value for	this data/parameter. If
	   "value" is missing a	1 is assumed (which is convenient for the
	   boolean options). If	"value"	starts with "@"	it is treated as a
	   local filename, and its contents is used as the data/parameter

       hash reference
	   The same as with the	array reference	but now	there is no need to
	   use an equal	sign. The hash keys are	input names and	hash values
	   their data. The values can again start with a "@" sign indicating a
	   local filename.

	Usage	: $tool->wait_for ( { 'sequence' => '@my,file' } )
	Returns	: $self
	Args	: the same as for method 'run'

       Create a	job, start it and wait for its completion. The method is
       identical to the	method "run". See details in the "run" method.

	Usage	: $tool->status
	Returns	: string describing a status of	the execution
	Args	: none

       It returns one of the following strings (and perhaps more if a server
       implementation extended possible	job states):

	  CREATED	       (not run	yet)
	  COMPLETED	       (run and	finished normally)
	  TERMINATED_BY_ERROR  (run and	finished with an error or a signal)

	Usage	: $job->result (...)
	Returns	: a result created by running an analysis
	Args	: none (but an implementation may choose
		  to add arguments for instructions how	to process
		  the raw result)

       The method returns a scalar representing	a result of an executed	job.
       If the job was terminated by an error the result	may contain an error
       message instead of the real data	(or both, depending on the

perl v5.32.0			  2019-12-07	       Bio::SimpleAnalysisI(3)


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