Bio::T...y::Base(3pm)

💖 Bio::T...y::Base(3pm) 💖

okay so bestie, this is the manual page Bio::T...y::Base(3pm) from the User Contributed Perl Documentation, and the module it's actually out here documenting is Bio::Tools::Run::Phylo::Hyphy::Base 🦋 it's giving "wrapper glue for HyPhy" and honestly? we love a base class that knows its job. let's get into it 💅

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✨ NAME ✨

Bio::Tools::Run::Phylo::Hyphy::Base — Hyphy wrapping base methods 🧬

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🎀 SYNOPSIS 🎀

FIXME

not the FIXME bestie 😭 that's literally the entire synopsis. it's giving "we'll fill this in later" and later never showed up. but it IS what the page says, so here it is, untouched, no cap.

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🌸 DESCRIPTION 🌸

HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information. 🔥

like yes, that's the whole description. short, sweet, points you at the website. iconic behavior honestly 👑

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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 💖

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 responsive 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/

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👑 AUTHOR - Albert Vilella 👑

Email avilella-at-gmail-dot-com 📧

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here

yes bestie, that's literally the placeholder text. it's giving "the contributors are a mystery" 🙈

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🧚 APPENDIX 🧚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ ✨

Default Values

Valid and default values are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the python wrapper or provided by the author. 🎀

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program_name

• Title — program_name
• Usage — $factory->program_name()
• Function — holds the program name
• Returns — string
• Args — None

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valid_values

• Title — valid_values
• Usage — $factory->valid_values()
• Function — returns the possible parameters
• Returns — an array holding all possible parameters (this needs to be specified per child class). Returns an empty array in the base class.
• Args — None

so like, the base class is out here returning an empty array on purpose. it's the "I'm just the blueprint bestie" energy 💅

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program_dir

• Title — program_dir
• Usage — ->program_dir()
• Function — returns the program directory, obtained from ENV variable.
• Returns — string
• Args — (empty)

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new

• Title — new
• Usage — my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
• Function — Builds a new Bio::Tools::Run::Phylo::Hyphy object
• Returns — Bio::Tools::Run::Phylo::Hyphy
• Args —
  • -alignment — the Bio::Align::AlignI object
  • -save_tempfiles — boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE)
  • -tree — the Bio::Tree::TreeI object
  • -params — a hashref of parameters (all passed to set_parameter)
  • -executable — where the hyphy executable resides

See also: Bio::Tree::TreeI, Bio::Align::AlignI

heads up bestie, -save_tempfiles defaults to FALSE, so if you don't flip it, your tempfiles get cleaned up and NOT kept. don't say I didn't warn you 🙈

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prepare

• Title — prepare
• Usage — my $rundir = $hyphy->prepare($aln);
• Function — prepare the analysis using the default or updated parameters; the alignment parameter must have been set
• Returns — value of rundir
• Args — L<Bio::Align::AlignI> object, L<Bio::Tree::TreeI> object [optional]

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create_wrapper

• Title — create_wrapper
• Usage — $self->create_wrapper
• Function — It will create the wrapper file that interfaces with the analysis bf file
• Example — (empty)
• Returns — (empty)
• Args — (empty)

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run

• Title — run
• Usage — my ($rc,$results) = $BatchFile->run();
• Function — run the Hyphy analysis using the specified batchfile and its ordered parameters
• Returns — Return code, Hash
• Args — none

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error_string

• Title — error_string
• Usage — $obj->error_string($newval)
• Function — Where the output from the last analysis run is stored.
• Returns — value of error_string
• Args — newvalue (optional)

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alignment

• Title — alignment
• Usage — $hyphy->alignment($aln);
• Function — Get/Set the L<Bio::Align::AlignI> object
• Returns — L<Bio::Align::AlignI> object
• Comment — We could potentially add support for running directly on a file but we shall keep it simple
• See also — L<Bio::SimpleAlign>

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tree

• Title — tree
• Usage — $hyphy->tree($tree);
• Function — Get/Set the L<Bio::Tree::TreeI> object
• Returns — L<Bio::Tree::TreeI>
• Args — [optional] $tree => L<Bio::Tree::TreeI>,
• Comment — We could potentially add support for running directly on a file but we shall keep it simple
• See also — L<Bio::Tree::Tree>

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get_parameters

• Title — get_parameters
• Usage — my %params = $self->get_parameters();
• Function — returns the list of parameters as a hash
• Returns — associative array keyed on parameter names
• Args — none

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set_parameter

• Title — set_parameter
• Usage — $hyphy->set_parameter($param,$val);
• Function — Sets a hyphy parameter, will be validated against the valid values. The checks can be ignored if one turns off param checks like this:

$hyphy->no_param_checks(1)

• Returns — boolean if set was success, if verbose is set to -1 then no warning will be reported
• Args —
  • $param => name of the parameter
  • $value => value to set the parameter to

See also: L<no_param_checks()>

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set_default_parameters

• Title — set_default_parameters
• Usage — $obj->set_default_parameters();
• Function — (Re)set the default parameters from the defaults (the first value in each array in the valid_values() array)
• Returns — none
• Args — none

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update_ordered_parameters

• Title — update_ordered_parameters
• Usage — $hyphy->update_ordered_parameters(0);
• Function — (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable)
• Returns — none
• Args — boolean: keep existing parameter values

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outfile_name

• Title — outfile_name
• Usage — my $outfile = $hyphy->outfile_name();
• Function — Get/Set the name of the output file for this run (if you wanted to do something special)
• Returns — string
• Args — [optional] string to set value to

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version

• Title — version
• Usage — $obj->version()
• Function — Returns the version string from HYPHY
• Returns — string
• Args — none

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hyphy_lib_dir

• Title — hyphy_lib_dir
• Usage — $obj->hyphy_lib_dir()
• Function — Returns the HYPHY_LIB_DIRECTORY from HYPHY
• Returns — string
• Args — none

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and that's the whole page bestie 💜 it went out with perl v5.36.0 dated 2023-01-22, under the manual name Bio::T...y::Base(3pm) 🎀 go forth and wrap some HyPhy, you absolute main character 👑✨