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

💖 NAME 💖

Bio::Tools::Run::Phylo::Phylip::DrawTree — bestie, this is the module that drives Joe Felsenstein's Phylip DrawTree program to draw your trees ✨ (and yeah, the man page header truncates it to Bio::T...awTree(3pm) under User Contributed Perl Documentation — she's long, ok?)

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✨ SYNOPSIS ✨

use Bio::Tools::Run::Phylo::Phylip::DrawTree;

my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
my $treeimagefile = $drawfact->run($tree);

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🌸 DESCRIPTION 🌸

Okay so, this is the module that automates drawing of trees through Joe Felsenstein's Phylip suite. Iconic of it, honestly. 💅

To set parameters with an option you need to pass in an array reference or a string, depending on the parameter. Like, they're not all the same shape, so pay attention. For example:

$treedraw->HORIZMARGINS(['2.00','2.5']);
$treedraw->ANCESTRALNODES('C');
$treedraw->TREESTYLE('PHEN');
$treedraw->USEBRANCHLENS('N');

Ngl, this can be a brittle module, because the menus change in PHYLIP 😭. It should support phylip 3.6 but no guarantees. No cap. So if it acts up on some other version, that's why.

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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, 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. 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 - Jason Stajich 👑

Email jason-at-bioperl.org — yeah, that's the human behind all this. King behavior. 🌈

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, that underscore means don't touch unless you know what you're doing 💀).

program_name

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

program_dir

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

new

• Title: new
• Usage: my $obj = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
• Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawTree object
• Returns: an instance of Bio::Tools::Run::Phylo::Phylip::DrawTree
• Args: The available DrawGram parameters

run

• Title: run
• Usage: my $file = $app->run($treefile);
• Function: Draw a tree
• Returns: File containing the rendered tree
• Args: either a Bio::Tree::TreeI

OR

filename of a tree in newick format

draw_tree

• Title: draw_tree
• Usage: my $file = $app->draw_tree($treefile);
• Function: This method is deprecated. Please use run method. (Ma'am, please retire her 😭)
• Returns: File containing the rendered tree
• Args: either a Bio::Tree::TreeI

OR

filename of a tree in newick format

_run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to drawgram program
• Example:
• Returns: Bio::Tree object
• Args: Name of a file the tree to draw in newick format and a parameter string to be passed to drawgram

_setinput()

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for drawing program
• Example:
• Returns: filename containing tree in newick format
• Args: Bio::Tree::TreeI object

_setparams()

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for drawgram program
• Example:
• Returns: parameter string to be passed to drawgram
• 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 = $dragram->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 DrawTree run
• Returns: none
• Args: none

io

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

See Bio::Root::IO

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And that's the whole page, bestie 🧚 — this lil doc came to you from perl v5.36.0, dated 2023-01-22, under the name Bio::T...awTree(3pm) in the User Contributed Perl Documentation. Go draw some trees, you absolute main character 👑✨