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

💖 NAME 💖

Bio::Tools::Run::Phylo::Phylip::DrawGram — bestie, this is the module that lets you use the Phylip DrawTree program to draw phylograms or phenograms. 🌳✨

(and yes, the manual name up top is Bio::T...awGram(3pm) from the User Contributed Perl Documentation crew 🫶)

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🌸 SYNOPSIS 🌸

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

my $drawfact = Bio::Tools::Run::Phylo::Phylip::DrawGram->new();
my $treeimage = $drawfact->run($tree);

Like, two lines and you have a tree pic. Iconic behaviour, no notes. 💅

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🦋 DESCRIPTION 🦋

This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite. That's it, that's the whole vibe — it wraps the whole tree-drawing situation so you don't have to wrangle it yourself. 🎀

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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 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, they eat that up) 💜

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 (yes bestie, the original writes it with the dashes, keep it exactly like that 💖)

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, underscore means hands off 🙈)

program_name

• Title: program_name
• Usage: >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:

new

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

The main character constructor moment. 🌟

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 instead.
• Returns: File containing the rendered tree
• Args: either a Bio::Tree::TreeI OR filename of a tree in newick format

⚠️ Deprecated alert! It still exists, but bestie, use run instead. The old one is giving legacy energy. 💀

_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 DrawGram 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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okay that's the whole page bestie, you ate that 🍓✨

this one's from perl v5.36.0, dated 2023-01-22, and the manual tag on the tin is Bio::T...awGram(3pm) 💅 mwah, go draw some trees 🌳🦋💖