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

📦

version 1.7.3 · 3 versions

1.7.3 · debian bookworm, ubuntu noble (latest)
1.7.3 · ubuntu jammy
1.7.3 · debian trixie

✨ NAME ✨

Bio::Tools::Run::Phylo::Phast::PhastCons — bestie, it's a wrapper for footprinting with phastCons 💖 (this is from the User Contributed Perl Documentation, so you know it's the real deal)

🌸 SYNOPSIS 🌸

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

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

# Pass the factory an alignment and the corresponding species tree
$align_filename = 't/data/apes.multi_fasta';
$species_tree_filename = 't/data/apes.newick';
@features = $factory->run($align_filename, $species_tree_filename);

# or get a Bio::Align::AlignI (SimpleAlign) object from somewhere, and
# generate the species tree automatically using a Bio::DB::Taxonomy database
$tdb = Bio::DB::Taxonomy->new(-source => 'entrez');
@features = $factory->run($aln_obj, $tdb);

# @features is an array of Bio::SeqFeature::Annotated, one feature per
# alignment sequence and prediction

🦋 DESCRIPTION 🦋

okay so this is a wrapper for running the phastCons application by Adam Siepel. the details live here: http://compgen.bscb.cornell.edu/~acs/software.html — and phastCons is what you use for phylogenetic footprinting / shadowing. it's giving evolutionary detective work, fr fr 👑

righhhht now the interface is extremely simplified, and it only lets you do one analysis method. the whole vibe here is ease of use: let phastCons estimate as many parameters as it possibly can, and have it output just the 'most conserved' blocks it detects. that said, you can try feeding it normal phastCons arguments to new(), or calling arg-named methods (drop the leading hyphens, turn the rest into underscores — like $factory->indels_only(1) to set the --indels-only arg). slay ✨

the particular analysis carried out here is to:

Use phyloFit to generate a tree model for initialization of the nonconserved model from the supplied alignment (all data) and species tree
Run phastCons in 'training' mode for parameter estimation using all the alignment data and the model from step 1
Run phastCons with the trees from step 2 to discover the most conserved regions

see the 'HowTo' at http://compgen.bscb.cornell.edu/~acs/phastCons-HOWTO.html for details on how to improve results. iykyk 💅

⚠️ WARNING: the API is likely to change in the future to allow for alternative analysis types. not me warning you ahead of time 😭

you will need to enable this phastCons wrapper to find the phast programs (at least phastCons and phyloFit). this can be done in (at least) three ways:

Make sure the phastCons and phyloFit executables are in your path.
Define an environmental variable PHASTDIR which is a directory which contains the phastCons and phyloFit applications: In bash:

export PHASTDIR=/home/username/phast/bin

In csh/tcsh:

setenv PHASTDIR /home/username/phast/bin

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

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

💌 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. (yes the original says "reponsive", we keep it, no cap 🫡)

🐛 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/

👑 AUTHOR - Sendu Bala 👑

Email bix@sendu.me.uk

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _

⭐ 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::PhastCons->new(@params)
Function: Creates a new PhastCons factory
Returns : Bio::Tools::Run::Phylo::Phast::PhastCons
Args    : Optionally, provide any of the following (defaults are not to use,
          see the same-named methods for information on what each option does):
          {
           -target_coverage  => number between 0 and 1
           AND
           -expected_length  => int
          }
          -rho => number between 0 and 1
          -quiet => boolean (turn on or off program output to console)

          Most other options understood by phastCons can be supplied as key =>
          value pairs in this way. 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. '--indels-only' => 1) or with only a single
          hyphen to start and internal hyphens converted to underscores (eg.
          -indels_only => 1) to avoid having to quote the key.

          These options can NOT be used with this wrapper currently:
          estimate_trees / T
          estimate_rho / O
          gc / G
          msa_format / i
          score / s
          no_post_probs / n
          seqname / N
          idpref / P
          help / h
          alias / A
          most_conserved / V / viterbi
          refidx / r

⭐ target_coverage ⭐

Title   : target_coverage
Usage   : $factory->target_coverage(0.25);
Function: Constrain transition parameters such that the expected fraction of
          sites in conserved elements is the supplied value.
Returns : number (default undef)
Args    : None to get, number (between 0 and 1) to set

⭐ expected_length ⭐

Title   : expected_length
Usage   : $factory->expected_length(5);
Function: Set transition probabilities such that the expected length of a
          conserved element is the supplied value. target_coverage() must also
          be set.
Returns : int (default undef)
Args    : None to get, int to set

⭐ rho ⭐

Title   : rho
Usage   : $factory->rho(0.3);
Function: Set the *scale* (overall evolutionary rate) of the model for the
          conserved state to be the supplied number times that of the model for
          the non-conserved state (default 0.3).
Returns : number (default undef)
Args    : None to get, number (between 0 and 1) to set

⭐ 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 phastCons on an alignment to find the most conserved regions
          ('footprinting').
Returns : array of Bio::SeqFeature::Annotated (one feature per alignment
          sequence and prediction)
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 file name for result production, AND filename of phyloFit
          generated init.mod file to estimate trees

okay that's the whole page bestie, you're so welcome 💜 this one shipped with perl v5.36.0 and was dated 2023-01-22 — main character energy from the User Contributed Perl Documentation crew, periodt 🎀✨

📦 where this page comes from

debian bookworm: libbio-perl-run-perl 1.7.3-9 · Perl
ubuntu noble: libbio-perl-run-perl 1.7.3-9 · Perl
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms