Bio::Tools::Run::Analysis(3) Module representing any (remote or local)


# 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...
} )
# 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";
# prints (for example):
# edit::seqret/c8ef56:ef535489ac:-7ff4
# 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",
'Finished: ' . $job->ended (1), # (1) means 'formatted'
'Elapsed time: ' . $job->elapsed,
$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",
# ...
# ...and later you may free this job resources
# --- See DESCRIPTION for using generator '':


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
  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')
  print $outseq;


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.

  [email protected]                  - General discussion  - About the mailing lists


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

[email protected]

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 ([email protected])


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.


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


 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:

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.

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

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

Default is "" ( services running at European Bioinformatics Institute on top of most of EMBOSS analyses, and on few others).

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").

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.
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 "" script.


 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:
             (and perhaps others)
           Additionally and specifically for this object:
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).
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 (...);


 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.


 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).


 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.