oracular (3) Bio::SimpleAnalysisI.3pm.gz
NAME
Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool
SYNOPSIS
This is an interface module - you do not instantiate it. Use other modules instead (those that implement
this interface).
DESCRIPTION
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).
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:
https://github.com/bioperl/bioperl-live/issues
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
• http://www.ebi.ac.uk/Tools/webservices/soaplab/guide
APPENDIX
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 message.
analysis_name
Usage : $tool->analysis_name;
Returns : a name of this analysis
Args : none
analysis_spec
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".
input_spec
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).
result_spec
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'
};
run
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 value.
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.
wait_for
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.
status
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)
result
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
implementation).