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 notimplemented 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).
perl v5.32.1 2021-08-15 Bio::SimpleAnalysisI(3pm)
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