plucky (3) Bio::Tools::Run::Analysis.3pm.gz
NAME
Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis tool
SYNOPSIS
# 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...
} )
->status;
# 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";
# ...it prints (for example):
# edit::seqret/c8ef56:ef535489ac:-7ff4
# ...in 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",
$job->status,
'Finished: ' . $job->ended (1), # (1) means 'formatted'
'Elapsed time: ' . $job->elapsed,
$job->last_event,
$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",
$job->status,
# ...
);
# ...and later you may free this job resources
$job->remove;
#
# --- See DESCRIPTION for using generator 'applmaker.pl':
#
DESCRIPTION
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 Seqret.pm
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')
->wait_for
->outseq
;
print $outseq;
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:
http://redmine.open-bio.org/projects/bioperl/
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/soaplab/Perl_Client.html
APPENDIX
Here is the rest of the object methods. Internal methods are preceded with an underscore _.
new
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:
-access
-location
-name
-httpproxy
-timeout
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.
-access
It indicates what lower-level module to load. Default is 'soap'. Other (but future) possibilities
may be:
-access => 'novella'
-access => 'local'
-location
A location of the service. The contents is access-specific (see details in the lower-level
implementation modules).
Default is "http://www.ebi.ac.uk/soaplab/services" ( services running at European Bioinformatics
Institute on top of most of EMBOSS analyses, and on few others).
-name
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").
-httpproxy
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.
-timeout
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 "analysis.pl" script.
new
Usage : my $job = Bio::Tools::Run::Analysis::Job->new
(-access => 'soap',
-name => 'edit.seqret',
-id => 'xxxyyy111222333'
);
Returns : a re-created object representing a job
Args : The same arguments as for Bio::Tools::Run::Analysis object:
-access
-location
-name
-httpproxy
-timeout
(and perhaps others)
Additionally and specifically for this object:
-id
-analysis
-id A job ID created some previous time and now used to re-create the same job (in order to re-gain
access to this job results, for example).
-analysis
A "Bio::Tools::Run::Analysis" object whose properties (such as "-access" and "-location" are used to
re-create this job object.
Module Bio::Tools::Run::Analysis::Utils
It contains several general utilities. These are "functions", not methods. Therefore call them like, for
example:
&Bio::Tools::Run::Analysis::Utils::format_time (...);
format_time
Usage : Bio::Tools::Run::Analysis::Utils::format_time ($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.
_load_access_module
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::$access
It prints an error on STDERR if it fails to find and load the module (for example, because of the
compilation errors in the module).
_guess_access
Usage : Bio::Tools::Run::Analysis::Utils::guess_access ($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. Remember that this method is called only if
there was no -access parameter which could tell directly what access method to use.