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

🌸 NAME 🌸

okay bestie, sit down, hydrate, and let me put you on to something iconic: Bio::Tools::Run::Phylo::Phylip::Consense — it's a wrapper for the phylip program Consense. That's the whole assignment. It's part of the User Contributed Perl Documentation crew (yes, that's where you're reading this from, Bio::T...nsense(3pm) fr fr), so you already know the community said "we'll document this ourselves, periodt" 💅

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✨ SYNOPSIS ✨

here's the entire glow-up journey from "i have an alignment" to "i have a cute little tree picture", no steps skipped:

use Bio::Tools::Run::Phylo::Phylip::Consense;
use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
use Bio::Tools::Run::Phylo::Phylip::ProtDist;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;
use Bio::Tools::Run::Phylo::Phylip::DrawTree;

#first get an alignment
my $aio= Bio::AlignIO->new(-file=>$ARGV[0],-format=>"clustalw");
my $aln = $aio->next_aln;

# To prevent truncation of sequence names by PHYLIP runs, use set_displayname_safe
my ($aln_safe, $ref_name)=$aln->set_displayname_safe();

#next use seqboot to generate multiple aligments
my @params = ('datatype'=>'SEQUENCE','replicates'=>10);
my $seqboot_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);

my $aln_ref= $seqboot_factory->run($aln);

Or, for long sequence names:

my $aln_ref= $seqboot_factory->run($aln_safe);

#next build distance matrices and construct trees
my $pd_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
my $ne_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();

foreach my $a (@{$aln_ref}){
  my $mat = $pd_factory->create_distance_matrix($a);
  push @tree, $ne_factory->create_tree($mat);
}

#now use consense to get a final tree
my $con_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();

#you may set outgroup either by the number representing the order in
#which species are entered or by the name of the species

$con_factory->outgroup(1);
$con_factory->outgroup('HUMAN');

my $tree = $con_factory->run(\@tree);

# Restore original sequence names, after ALL phylip runs:
my @nodes = $tree->get_nodes();
foreach my $nd (@nodes){
   $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
}

#now draw the tree
my $draw_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
my $image_filename = $draw_factory->draw_tree($tree);

lowkey note from the source: set_displayname_safe is the move if you don't want PHYLIP truncating your sequence names, and you restore the real names at the very end, after ALL the phylip runs. don't skip the finale, bestie 🎀

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🔥 DESCRIPTION 🔥

It's a wrapper for the phylip consense program. 🌈

Straight from the phylip documentation, here's the tea:

CONSENSE reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree. Right now it runs a whole family of consensus tree methods called the M[l] methods (Margush and McMorris, 1981). These include strict consensus and majority rule consensus. Basically the consensus tree is made of monophyletic groups that occur as often as possible in the data. Slay. 👑

If you want more documentation on using Consense and setting parameters, it lives in the phylip package. Go look, i'll wait. 🫶

💜 VERSION Support 💜

This wrapper currently supports v3.5 of phylip. There's also support for v3.6, but heads up: that's still experimental, because v3.6 is still under alpha release and not all functionalities maybe supported. So like, tread carefully, it's giving "beta boyfriend" energy. 🙈

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🫶 PARAMETERS FOR Consense 🫶

🦋 TYPE 🦋

• Title: TYPE
• Description: (optional) — only available in phylip v3.6

This program supports 3 types of consensus generation (the page says 3 and then lists four, i'm just the messenger 💀):

• MRe : Majority Rule (extended). Any set of species that appears in more than 50% of the trees is included. The program then considers the other sets of species in order of the frequency with which they have appeared, adding to the consensus tree any which are compatible with it until

and yes bestie, the source documentation literally just trails off on "until". iconic cliffhanger, no notes 🎀

• STRICT: A set of species must appear in all input trees to be included in the strict consensus tree.
• MR : A set of species is included in the consensus tree if it is present in more than half of the input trees.
• Ml : The user is asked for a fraction between 0.5 and 1, and the program then includes in the consensus tree any set of species that occurs among the input trees more than that fraction of then time. The Strict consensus and the Majority Rule consensus are extreme cases of the M[l] consensus, being for fractions of 1 and 0.5 respectively
• usage:

my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-type=>"Ml 0.7");

Defaults to MRe.

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🌿 ROOTED 🌿

• Title: ROOTED
• Description: (optional)

toggles between the default assumption that the input trees are unrooted trees, and the selection that says the tree is to be treated as a rooted tree and not re-rooted. Otherwise the tree gets treated as outgroup-rooted and will be re-rooted automatically at the first species encountered on the first tree (or at a species designated by the Outgroup option).

• usage:

my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-rooted=>1);

Defaults to unrooted.

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🌸 OUTGROUP 🌸

• Title: OUTGROUP
• Description: (optional)

It's in effect only if the Rooted option selection is not in effect. The trees will be re-rooted with a species of your choosing.

• usage

my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-outgroup=>2);

Defaults to first species encountered.

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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 one of the Bioperl mailing lists. Your participation is much appreciated, genuinely, it's not a vibe check you can skip 🥺

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. fr fr, the more detail the better, don't just say "it's broken" 💀

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track 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 - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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🧚 APPENDIX 🧚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (so if you see an underscore, bestie, that's a "do not touch, that's backstage" situation 🚫)

program_name

• Title: program_name
• Usage: $obj->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:

idlength

• Title: idlength
• Usage: $obj->idlength ($newval)
• Function:
• Returns: value of idlength
• Args: newvalue (optional)

run

Usage:

$inputfilename = 't/data/prot.treefile';
$tree= $Consense_factory->run($inputfilename);

or

$tree= $consense_factory->run(\@tree);

• Function: Create bootstrap sets of alignments
• Example:
• Returns: a Bio::Tree::Tree
• Args: either a file containing trees in newick format or an array ref of Bio::Tree::Tree

⚠️ Throws an exception if argument is not either a string (eg a filename) or a Bio::Tree::TreeI object. If argument is string, throws exception if file corresponding to string name can not be found. so like, hand it the right thing or it WILL yell at you, no cap.

_run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to Consense program
• Example:
• Returns: an array ref of Bio::Tree::Tree
• Args: Name of a file containing a set of tree in newick format and a parameter string to be passed to Consense

_setinput()

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for Consense program
• Example:
• Returns: name of file containing a trees in newick format
• Args: an array ref of Bio::Tree::Tree object or input file name

names()

• Title: names
• Usage: $tree->names(\%names)
• Function: get/set for a hash ref for storing names in matrix with rank as values.
• Example:
• Returns: hash reference
• Args: hash reference

_setparams()

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for Consense program
• Example:
• Returns: parameter string to be passed to Consense
• Args: name of calling object

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🧬 Bio::Tools::Run::Wrapper methods 🧬

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:
• Returns: value of save_tempfiles
• Args: newvalue (optional)

outfile_name

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

cleanup

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

io

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

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and that's the whole page, bestie, you ate it 💖 This lil' slice of documentation comes from the User Contributed Perl Documentation for Bio::T...nsense(3pm), generated by perl v5.36.0 and dated 2023-01-22. go build a consensus tree, you absolute icon 👑🌸✨