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

💖 Bio::Tools::Run::Phylo::FastTree 💖

okay bestie, welcome to the Bio::Tools::Run::Phylo::FastTree page — it's part of the User Contributed Perl Documentation collection, and it's basically the lil glow-up machine that turns your DNA into a tree. no cap. 🌳✨

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::FastTree — it's giving Bio::Tree getter from DNA alignment. literally that's the whole job. 💅

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🦋 SYNOPSIS 🦋

okay so here's the vibe, copy-paste energy:

# Build a FastTree factory
$factory = Bio::Tools::Run::Phylo::FastTree->new(-quiet => 1,
                                                 -fastest => 1);
# Get an alignment
my $alignio = Bio::AlignIO->new(
      -format => 'fasta',
      -file   => '219877.cdna.fasta');
my $alnobj = $alignio->next_aln;

# Analyze the aligment and get a Tree
my $tree = $factory->run($alnobj);

(and yes the comment says "aligment", we love her, we keep her exactly as she is 🫶)

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🎀 DESCRIPTION 🎀

You hand it a protein or DNA alignment, you get back a Bio::Tree object. that's it. that's the whole main character arc. 👑

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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. (fr fr, they actually read these 💖)

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

Do not contact the module maintainer directly. no bestie, don't do it 😭

Many experienced experts at bioperl-l 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. (the more deets the better, give them the whole story 💀)

🐛 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 - Brian Osborne ✨

Email briano@bioteam.net

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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 it starts with an underscore, it's lowkey private business 🙈).

🌟 new 🌟

Title   : new
Usage   : my $treebuilder = Bio::Tools::Run::Phylo::FastTree->new();
Function: Constructor
Returns : Bio::Tools::Run::Phylo::FastTree
Args    : -outfile_name => $outname

she's the constructor, she makes the thing. that's her whole deal. ✨

🌟 program_name 🌟

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

🌟 program_dir 🌟

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory
Returns:  string
Args    :

🌟 error_string 🌟

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

(yes it says "analysus" — iconic typo, we're keeping her 💅)

🌟 version 🌟

Title   : version
Usage   : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args    : none

🌟 run 🌟

Title   : run
Usage   : $factory->run($stockholm_file) OR
          $factory->run($align_object)
Function: Runs FastTree to generate a tree
Returns : Bio::Tree::Tree object
Args    : File name for your input alignment in stockholm format, OR
          Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).

this is the one you actually call, bestie. drop in a stockholm file name or a Bio::Align::AlignI compliant object (like Bio::SimpleAlign), get a Bio::Tree::Tree back. ate. 🔥

🌟 _run 🌟

Title   : _run
Usage   : Internal function, not to be called directly
Function: Runs the application
Returns : Tree object
Args    : Alignment file name

internal function, not to be called directly. hands off, she's not for you 🙈

🌟 _write_alignfile 🌟

Title   : _write_alignfile
Usage   : Internal function, not to be called directly
Function: Create an alignment file
Returns : filename
Args    : Bio::Align::AlignI

also internal, also not to be called directly. noted. 📝

🌟 _alphabet 🌟

Title   : _alphabet
Usage   : my $alphabet = $self->_alphabet;
Function: Get the alphabet of the input alignment, defaults to 'dna'
Returns : 'dna' or 'protein'
Args    : Alignment file

defaults to 'dna' btw, so if you're a protein girlie you gotta say so 🧬

🌟 _setparams 🌟

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

internal. don't call it. you know the drill by now. 💀

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🧚 Bio::Tools::Run::BaseWrapper 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)

it's a boolean flag about whether we trust the sanity checks. make good choices. 🌈

💜 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 = $FastTree->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

if you wanted to do something special ✨ get/set the output file name, go off.

💜 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

heads up: calling this creates the temp directory. it's not just a lil peek, it's a whole birth. 👑

💜 cleanup 💜

Title   : cleanup
Usage   : $FastTree->cleanup();
Function: Will cleanup the tempdir directory
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

gets you a Bio::Root::IO object. iykyk. 🎀

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and that's the whole page bestie, you're officially FastTree literate 💅✨

perl v5.36.0 · 2023-01-22 — shoutout to the Bioperl crew for this one, mwah 🫶💖🌸