Bio::S...lysisI(3pm)

💖 NAME 💖

Bio::SimpleAnalysisI — a simple interface to any (local or remote) analysis tool. Yes bestie, any. Local, remote, doesn't matter, she's flexible like that. 🌈

This page lives in the User Contributed Perl Documentation section, and the manual is Bio::S...lysisI(3pm) — yes the name is literally truncated like that, the vibes are mysterious, we love a cryptic queen. 💅

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✨ SYNOPSIS ✨

Okay so heads up: this is an interface module — you do NOT instantiate it. Like, ever. Use other modules instead, specifically the ones that implement this interface. She's the blueprint, not the building. 🏗️

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🦋 DESCRIPTION 🦋

This interface contains the public methods for accessing and controlling local and remote analysis tools. It's meant to be used on the client side, iykyk. 💅

The interface consists only of a necessary set of methods for synchronous invocation of analysis tools. If you want the more complex set — including asynchronous access — go look at the interface Bio::AnalysisI (which inherits from this one, btw. nepotism but make it OOP 🫶).

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📣 FEEDBACK 📣

🌸 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — literally, your comments are the glow-up. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, fr fr. 💖

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. The reason? Many experienced and responsive experts will be able to look at the problem and quickly address it. It's giving "ask the group chat, not the one person." 👑

Please include a thorough description of the problem with code and data examples if at all possible. No vague "it doesn't work" energy, we need the receipts. 📎

🐛 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

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👑 AUTHOR 👑

Martin Senger (martin.senger@gmail.com)

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⭐ 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. Slay, open source. 💅

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💀 DISCLAIMER 💀

This software is provided "as is" without warranty of any kind. No cap, no promises, no guarantees. 🙈

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🔥 SEE ALSO 🔥

• http://www.ebi.ac.uk/Tools/webservices/soaplab/guide

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🎀 APPENDIX 🎀

This is actually the main documentation... yes the appendix is the main character here, plot twist. ✨

If you try to call any of these methods directly on this Bio::SimpleAnalysisI object you will get a not implemented error message. She said "I'm an interface, I don't do labor." 😭

🧚 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 — and ngl, not all of them are always present, and perhaps others are 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 also be associated with a default value, with allowed values, and with a few other attributes. The names matter for feeding the analysis with the input data — the inputs are given to methods run and wait_for as name/value pairs. So like, remember the names, bestie. 📝

🧚 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. (Yes, "metod." We're keeping it, it's iconic. 💅)

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 are there two methods doing the exact same thing? Because it is expected that the sub-classes may implement them differently — an example is the interface Bio::AnalysisI, which uses method run for an asynchronous execution and method wait_for for a synchronous one. Two names, one vibe. 🦋

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 (and yes, "prameters" — we don't fix typos around here, we preserve them like artifacts 🏺):

• 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. (Told you, twins. 👯)

🧚 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). So like, check your status first, okay? 🚨

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And that's the whole page, bestie!! 💖 This was Bio::S...lysisI(3pm) from perl v5.32.1, dated 2021-08-15, straight outta the User Contributed Perl Documentation. Go forth and interface responsibly. Periodt. 💅✨