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

💖 Bio::T...hyloFit(3pm) 💖

okay bestie, this is a page from the User Contributed Perl Documentation — it's the manual for the Perl module Bio::Tools::Run::Phylo::Phast::PhyloFit, and yes the name is a whole mouthful, we're just gonna roll with it 🫶

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✨ NAME ✨

Bio::Tools::Run::Phylo::Phast::PhyloFit — it's a wrapper for phyloFit, no cap 💅

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🌸 SYNOPSIS 🌸

literally the whole vibe in four lines:

  use Bio::Tools::Run::Phylo::Phast::PhyloFit;

  # Make a PhyloFit factory
  $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new();

  # Generate an init.mod file for use by phastCons
  my $init_file = $factory->run($alignment, $tree);

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🦋 DESCRIPTION 🦋

so this whole thing is a wrapper for running the phyloFit application, which is by Adam Siepel 👑 you can get the details right here:

http://compgen.bscb.cornell.edu/~acs/software.html

Currently the interface is extremely simplified. Like, extremely. The only form of usage allowed is the --tree form (not --init-model), which means a tree must be supplied along with the alignment (to run()). You can try handing normal phyloFit arguments to new(), or call the arg-named methods (drop the leading hyphens and turn the other hyphens into underscores — e.g. $factory->gaps_as_bases(1) to set the --gaps-as-bases arg). iykyk 💅

⚠️ WARNING: the API may change in the future to allow for greater flexability and access to more phyloFit features. so like, don't get too attached to the current shape of things 😭

You will need to enable this PhyloFit wrapper to find the phast programs (at least phyloFit itself). This can be done in (at least) three ways:

1. Make sure the phyloFit executable is in your path. ✨
2. Define an environmental variable PHASTDIR which is a directory which contains the phyloFit application: In bash:

export PHASTDIR=/home/username/phast/bin

In csh/tcsh:

setenv PHASTDIR /home/username/phast/bin

3. Include a definition of an environmental variable PHASTDIR in every script that will use this PhyloFit wrapper module, e.g.:

BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
use Bio::Tools::Run::Phylo::Phast::PhyloFit;

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. So like, your thoughts matter here, genuinely 🥺 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'll 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 - Sendu Bala 👑

Email bix@sendu.me.uk

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (the underscore is basically the "don't talk to me, I'm internal" energy 🙈)

🔧 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, obtained from ENV variable.
 Returns : string
 Args    : None

🔧 new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::Phylo::Phast::PhyloFit->new()
 Function: creates a new PhyloFit factory
 Returns : Bio::Tools::Run::Phylo::Phast::PhyloFit
 Args    : Most options understood by phastCons can be supplied as key =>
           value pairs. Options that don't normally take a value
           should be given a value of 1. You can type the keys as you would on
           the command line (eg. '--gaps-as-bases' => 1) or with only a single
           hyphen to start and internal hyphens converted to underscores (eg.
           -gaps_as_bases => 1) to avoid having to quote the key.

           These options can NOT be used with this wrapper currently:
           msa_format / i
           out_root / o
           tree / t
           help / h
           lnl / L
           init_model / M
           scale_only / B
           scale_subtree / S
           no_freqs / f
           no_rates / n
           post_probs / P
           expected_subs / X
           expected_total_subs / Z
           column_probs / U
           windows / w
           windows_explicit / v

💀 heads up bestie: that list of options is a hard NO for this wrapper right now. not "maybe", not "if you're brave" — genuinely can NOT be used.

🔧 run

 Title   : run
 Usage   : $result = $factory->run($fasta_align_file, $newick_tree_file);
           -or-
           $result = $factory->run($align_object, $tree_object);
           -or-
           $result = $factory->run($align_object, $db_taxonomy_object);
 Function: Runs phyloFit on an alignment.
 Returns : filename of init.mod file produced
 Args    : The first argument represents an alignment, the second argument
           a species tree.
           The alignment can be provided as a multi-fasta format alignment
           filename, or a Bio::Align::AlignI compliant object (eg. a
           Bio::SimpleAlign).
           The species tree can be provided as a newick format tree filename
           or a Bio::Tree::TreeI compliant object. Alternatively a
           Bio::DB::Taxonomy object can be supplied, in which case the species
           tree will be generated by using the alignment sequence names as
           species names and looking for those in the supplied database.

           In all cases, the alignment sequence names must correspond to node
           ids in the species tree. Multi-word species names should be joined
           with underscores to form the sequence names, eg. Homo_sapiens

🔧 _setparams

 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: Creates a string of params to be used in the command string
 Returns : string of params
 Args    : alignment and tree file names

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okay that's the whole page, you made it, I'm so proud of you 🥹💖 this was built for perl v5.36.0 and last touched on 2023-01-22 — consider this your lil sign-off, go run phyloFit and slay ✨🎀🦋