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

💖 NAME

Bio::Tools::Run::Simprot — bestie, it's a wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree. That's the whole vibe 💅

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✨ SYNOPSIS

use Bio::Tools::Run::Simprot;
use Bio::TreeIO;

my $treeio = Bio::TreeIO->new(
    -format => 'nh', -file => 't/data/tree.nh');

my $tree = $treeio->next_tree;

my $simprot = Bio::Tools::Run::Simprot->new();
$simprot->tree($tree);
my ($rc,$aln,$seq) = $simprot->run();

okay so literally that's it, you just do that 🫶

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🌸 DESCRIPTION

So this is a wrapper around the Simprot program, and the icons who wrote it are Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier. obsessed with them, no cap ✨

Simprot lets you pick from several models of amino acid substitution — PAM, JTT and PMB — it allows for gamma distributed sites rates according to Yang's model, and it implements a parameterised Qian and Goldstein distribution model for insertion and deletion. it's giving versatile fr fr 🔥

See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more information.

🧚 Helping the module find your executable

You will need to enable SIMPROTDIR to find the simprot program. This can be done in (at least) three ways:

1. Make sure the simprot executable is in your path (i.e. 'which simprot' returns a valid program
2. define an environmental variable SIMPROTDIR which points to a directory containing the 'simprot' app:

In bash

export SIMPROTDIR=/home/progs/simprot   or

In csh/tcsh

setenv SIMPROTDIR /home/progs/simprot

3. include a definition of an environmental variable SIMPROTDIR in every script that will

BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
use Bio::Tools::Run::Simprot;

pick whichever one slaps for your setup, they all work 💫

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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. (like genuinely, they want to hear from you 🥺)

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. (the more deets you give, the faster someone can slay your bug 💅)

🔥 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 - Albert Vilella

Email avilella-at-gmail-dot-com 💌

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💅 APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk 🙈

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 :

new

• Title : new
• Usage : my $simprot = Bio::Tools::Run::Simprot->new();
• Function: Builds a new Bio::Tools::Run::Simprot
• Returns : Bio::Tools::Run::Simprot
• Args :
  • -alignment => the Bio::Align::AlignI object
  • -tree => the Bio::Tree::TreeI object
  • -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE)
  • -executable => where the simprot executable resides
  • -params => A reference to a hash where keys are parameter names and hash values are the associated parameter values

See also: Bio::Tree::TreeI, Bio::Align::AlignI

set_parameters

• Title : set_parameters
• Usage : $codeml->set_parameters($parameter, $value);
• Function: (Re)set the SimProt parameters
• Returns : none
• Args : First argument is the parameter name, second argument is the parameter value

set_default_parameters

• Title : set_default_parameters
• Usage : $codeml->set_default_parameters(0);
• Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable)
• Returns : none
• Args : boolean: keep existing parameter values

get_parameters

• Title : get_parameters
• Usage : my %params = $self->get_parameters();
• Function: returns the list of parameters as a hash
• Returns : associative array keyed on parameter names
• Args : none

prepare

• Title : prepare
• Usage : my $rundir = $simprot->prepare();
• Function: prepare the simprot analysis using the default or updated parameters, the alignment parameter and species tree must have been set
• Returns : value of rundir
• Args : L<Bio::Align::AlignI> object, L<Bio::Tree::TreeI> object [optional]

run

• Title : run
• Usage : my $nhx_tree = $simprot->run();
• Function: run the simprot analysis using the default or updated parameters, the alignment parameter must have been set
• Returns : L<Bio::Tree::TreeI> object [optional]
• Args : L<Bio::Align::AlignI> object, L<Bio::Tree::TreeI> object

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)

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

alignment

• Title : alignment
• Usage : $simprot->align($aln);
• Function: Get/Set the L<Bio::Align::AlignI> object
• Returns : L<Bio::Align::AlignI> object
• Args : [optional] L<Bio::Align::AlignI>
• Comment : We could potentially add support for running directly on a file but we shall keep it simple
• See also: L<Bio::SimpleAlign>

tree

• Title : tree
• Usage : $simprot->tree($tree, %params);
• Function: Get/Set the L<Bio::Tree::TreeI> object
• Returns : L<Bio::Tree::TreeI>
• Args : [optional] $tree => L<Bio::Tree::TreeI>, [optional] %parameters => hash of tree-specific parameters
• Comment : We could potentially add support for running directly on a file but we shall keep it simple
• See also: L<Bio::Tree::Tree>

Bio::Tools::Run::BaseWrapper methods

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 = $simprot->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 : $simprot->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

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and that's a wrap bestie 🎀✨ this page is from Bio::T...improt(3pm), part of the User Contributed Perl Documentation, running on perl v5.36.0 and dated 2023-01-22. go forth and simulate some sequences, you absolute icon 💖🦋💅