Bio::T...actory(3pm)

🦋 okay so bestie, welcome to Bio::Tools::Run::AnalysisFactory(3pm) 🦋

This is the manual page for Bio::Tools::Run::AnalysisFactory — the Perl module that's basically a whole directory of analysis tools. Pull up a chair, grab a boba, we're doing this. 💖

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🎀 NAME 🎀

Bio::Tools::Run::AnalysisFactory — a directory of analysis tools. That's the whole résumé, and honestly? Iconic.

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✨ SYNOPSIS ✨

Here's the whole vibe in code, no notes:

  # list all available analyses from the default location,
  # using a default (SOAP) access method
  use Bio::Tools::Run::AnalysisFactory;
  my $list = Bio::Tools::Run::AnalysisFactory->new();
                ->available_analyses;
  use Data::Dumper; print Dumper ($list);

  # ditto, but from a different location
  use Bio::Tools::Run::AnalysisFactory;
  my $list =
     Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something')
                ->available_analyses;

  # ...and using a different access method
  # (this example is not yet impelmented)
  use Bio::Tools::Run::AnalysisFactory;
  my $list =
     Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something',
                                           -access => 'novella')
                ->available_analyses;

  # list available categories of analyses
  use Bio::Tools::Run::AnalysisFactory;
  my $categories =
     Bio::Tools::Run::AnalysisFactory->new();
                ->available_categories;
  use Data::Dumper; print Dumper ($categories);

  # show all analyses group by categories
  use Bio::Tools::Run::AnalysisFactory;
  my $factory = Bio::Tools::Run::AnalysisFactory->new();
  foreach $cat ( @{ $factory->available_categories } ) {
    my @sublist = @{ $factory->available_analyses ($cat) };
    print "$cat:\n\t",
          join ("\n\t", @{ $factory->available_analyses ($cat) }),
          "\n";
  }

  # create an analysis object
  use Bio::Tools::Run::AnalysisFactory;
  $service = Bio::Tools::Run::AnalysisFactory->new();
                 ->create_analysis ('edit.seqret');
  $service->run (
                #...
                )->results;

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💜 DESCRIPTION 💜

okay so here's the tea, fr fr. 🍓

• The module represents a list of available analysis tools from a given location using a given access method. And on top of that, for any of the available analyses, it can create an object of type Bio::Tools::Run::Analysis. So it's giving directory and factory. Multitasking queen. 👑
• It's a higher-level abstraction whose main job is to load a 'real-work-doing' implementation. Which one actually gets used? Depends on the -access parameter. Same design as the Bio::Tools::Run::Analysis module — consistent, we love a theme. ✨
• There is available a SOAP access to almost all EMBOSS applications, running at European Bioinformatics Institute. Yes, that's a whole thing you can just... use.
• The documentation of all "public" methods are to be found in Bio::Factory::AnalysisI. Go read that one next, bestie.

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📬 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. (Yes, they mean you. 🫶)

  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. (Basically: show your work, bestie, it helps the experts help you.)

🐛 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/

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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.

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💀 DISCLAIMER 💀

This software is provided "as is" without warranty of any kind.

No cap. That's literally what it says. 🫠

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🌈 SEE ALSO 🌈

• http://www.ebi.ac.uk/soaplab/Perl_Client.html

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🧚 APPENDIX 🧚

Here is the rest of the object methods. Internal methods are preceded with an underscore _. (iykyk — if it starts with an underscore, it's private business. 🙈)

🌟 new

Usage   : my $factory =
            Bio::Tools::Run::AnalysisFactory->new(-access => 'soap',
                                                  -location => 'http://...');
Returns : a new Bio::Tools::Run::AnalysisFactory object representing a list
          of available analyses
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::AnalysisFactory::soap for a SOAP-based access).

          The recognised and used arguments are:
            -access
            -location
            -httpproxy
            -timeout

It builds, populates and returns a new Bio::Tools::Run::AnalysisFactory object. That's how it's seen from the outside. But in fact, it builds, populates and returns a more specific lower-level object, for example a Bio::Tools::Run::AnalysisFactory::soap object — which one it is, it depends on the -access parameter. Sneaky? No, just ✨architecture✨.

• -access — it indicates what lower-level module to load. Default is 'soap'. Other (but future) possibilities are:

  -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 (there are services running at European Bioinformatics Institute on top of most of EMBOSS analyses, and on some others).

• -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.

🔧 _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::AnalysisFactory::$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). So like, it will tell you, loudly. 😭

🔮 _guess_access

Usage   : $class->_guess_access ($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. (So it's the backup plan. The understudy. The main character when nobody else shows up. 💅)

📌 VERSION and Revision

Usage   : print $Bio::Tools::Run::AnalysisFactory::VERSION;
          print $Bio::Tools::Run::AnalysisFactory::Revision;

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and that's the whole page, bestie — you ate that. 🫶

This was Bio::Tools::Run::AnalysisFactory(3pm), brought to you by perl v5.32.1, dated 2021-08-15. Go forth and list some analyses. 💖✨🎀