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

💖 Bio::T...Evolver(3pm) — the manual page, but make it make sense 💖

okay bestie, gather round 🫶 this is Bio::T...Evolver(3pm) out of the User Contributed Perl Documentation corner of the world, and honestly? it's giving "genius wrapper with a documentation glow-up still pending". let's get into it 💅

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✨ NAME ✨

Bio::Tools::Run::Phylo::PAML::Evolver — a wrapper around the PAML program evolver. yes, the original literally says "Wrapper aroud" (typo and all 💀) but we know what it means, it wraps evolver, periodt.

🎀 VERSION 🎀

version 1.7.3 ✨

🌸 SYNOPSIS 🌸

lowkey the whole vibe in one code block, no notes:

use Bio::Tools::Run::Phylo::PAML::Evolver;

my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new();

# Get a $tree object somehow
$evolver->tree($tree);

# FIXME: evolver generates a tree (first run with option 1 or 2)?

# One or more alns are created
my @alns = $evolver->run();

####

# Or with all the data coming from a previous PAML run
my $parser = Bio::Tools::Phylo::PAML->new
  (
   -file => "$inputfile",
  );
my $result = $parser->next_result();
my $tree = $result->next_tree;
$evolver->tree($tree);
my @codon_freqs = $result->get_CodonFreqs();
$evolver->set_CodonFreqs(\@codon_freqs);

my $val = $evolver->prepare();

# FIXME: something similar for nucleotide frequencies:
# Option (5) Simulate nucleotide data sets (use MCbase.dat)?

# FIXME: something similar for aa parameters:
# Option (7) Simulate amino acid data sets (use MCaa.dat)?

# FIXME: With an initial RootSeq.txt

so many # FIXME:s in there 😭 the module is out here being honest about what it hasn't done yet and honestly? relatable. iconic, even.

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🦋 DESCRIPTION 🦋

okay so this module is a wrapper around the evolver program from PAML — that's Phylogenetic Analysis by Maximum Likelihood, the package by Ziheng Yang 👑. want more info? hit up:

http://abacus.gene.ucl.ac.uk/software/paml.html

the real main character energy here: this module is more about generating the properl (yes, that's the original spelling, we're keeping it 💀) MCmodel.ctl file, and it will run the program in a separate temporary directory so it doesn't leave temp files all over the place. clean girl aesthetic, we love to see it 🧚

🍓 Default Values 🍓

valid and default values for evolver programs are listed below. the default values are always the first one listed. these descriptions are essentially lifted from the example MCcodon.dat file and the pamlDOC documentation provided by the author — so credit where credit's due 💖

stub:

• option1 specifies something.
• option2 specifies something else.

INCOMPLETE DOCUMENTATION OF ALL METHODS — screaming, crying, throwing up 😭 the original says it, so we say it too. this page is a work in progress and we respect the honesty.

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👑 ATTRIBUTES 👑

💜 program_name

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

💜 program_dir

• Title: program_dir
• Usage: ->program_dir()
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args: (nothing given in the original)

💜 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)

💜 alignment

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

💜 tree

• Title: tree
• Usage: $evolver->tree($tree, %params);
• Function: Get/Set the L<Bio::Tree::TreeI> object
• Returns: L<Bio::Tree::TreeI>
• Args:

[optional] $tree => L<Bio::Tree::TreeI>,
[optional] %parameters => hash of tree-specific parameters:
       branchLengths: 0, 1 or 2
       out

• Comment: We could potentially add support for running directly on a file but we shall keep it simple
• See also: L<Bio::Tree::Tree>

💜 no_param_checks

• Title: no_param_checks
• Usage: $obj->no_param_checks($newval)
• Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values
• Returns: value of no_param_checks
• Args: newvalue (optional)

💜 save_tempfiles

• Title: save_tempfiles
• Usage: $obj->save_tempfiles($newval)
• Function: (blank in the original — we're not making anything up bestie)
• Returns: value of save_tempfiles
• Args: newvalue (optional)

💜 outfile_name

• Title: outfile_name
• Usage: my $outfile = $evolver->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

💜 tempdir

• Title: tempdir
• Usage: my $tmpdir = $self->tempdir();
• Function: Retrieve a temporary directory name (which is created)
• Returns: string which is the name of the temporary directory
• Args: none

💜 indel

• Title: indel
• Usage: $obj->indel($newval)
• Function: this is only useful if using evolver_indel instead of main evolver package: Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees — Brandi L. Cantarel, Hilary G. Morrison and William Pearson
• Example: (blank in the original)
• Returns: value of indel (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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💅 METHODS 💅

🌈 new

• Title: new
• Usage: my $obj = Bio::Tools::Run::Phylo::PAML::Evolver->new();
• Function: Builds a new Bio::Tools::Run::Phylo::PAML::Evolver object
• Returns: Bio::Tools::Run::Phylo::PAML::Evolver

-save_tempfiles => boolean to save the generated tempfiles and
                   NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object (FIXME: optional if this is done in a first run)
-params => a hashref of PAML parameters (all passed to set_parameter)
-executable => where the evolver executable resides

• See also: Bio::Tree::TreeI

ngl -save_tempfiles has "onesself" in it and we are NOT touching it, that's part of the lore now 🫶

🌈 prepare

• Title: prepare
• Usage: my $rundir = $evolver->prepare($aln);
• Function: prepare the evolver 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]

🌈 run

• Title: run
• Usage: my ($rc,$parser) = $evolver->run();
• Function: run the evolver analysis using the default or updated parameters. the alignment parameter must have been set
• Returns: Return code, L<Bio::Tools::Phylo::PAML>
• Args:

L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]

🌈 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

🌈 set_parameter

• Title: set_parameter
• Usage: $evolver->set_parameter($param,$val);
• Function: Sets a evolver parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if one turns off param checks like this:

$evolver->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()>

🌈 set_default_parameters

• Title: set_default_parameters
• Usage: $evolver->set_default_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

🌈 set_CodonFreqs

• Title: set_CodonFreqs
• Usage: $obj->set_CodonFreqs($newval)
• Function: Get/Set the Codon Frequence table
• Returns: value of set_CodonFreqs (a scalar)
• Args: on set, new value (a scalar or undef, optional)

🌈 get_CodonFreqs

• Title: get_CodonFreqs
• Usage: my @codon_freqs = $evolver->get_CodonFreqs()
• Function: Get the Codon freqs
• Returns: Array
• Args: none

🌈 cleanup

• Title: cleanup
• Usage: $evolver->cleanup();
• Function: Will cleanup the tempdir directory after a PAML run
• Returns: none
• Args: none

🌈 io

• Title: io
• Usage: $obj->io($newval)
• Function: Gets a L<Bio::Root::IO> object
• Returns: L<Bio::Root::IO>
• Args: none

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Bio::Tools::Run::WrapperBase methods — yeah, this line is just vibing on its own in the original, so it's vibing here too ✨

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💌 FEEDBACK 💌

📬 Mailing lists

user feedback is an integral part of the evolution of this and other Bioperl modules (the way that evolution pun works here... ate 💅). 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/Support.html    - 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 (their spelling, we're keeping it 😭) 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 — that's the cheat code for getting help fast, no cap.

🐛 Reporting bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bio-tools-phylo-paml/issues

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🌟 AUTHOR 🌟

Albert Vilella <avilella@gmail.com>

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📜 COPYRIGHT 📜

this software is copyright (c) by Albert Vilella <avilella@gmail.com>.

this software is available under the same terms as the perl 5 programming language system itself.

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and that's the whole page bestie 🎀 one last thing before you go: this manual page is perl v5.34.0, dated 2022-10-14, and it lives under the name Bio::T...Evolver(3pm) — yes it's truncated in the footer, we don't make the rules 💀 go generate some alignments, you've got this, mwah 💋✨