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 web:


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 message.


 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 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.


 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 implementation).