--- name: "Bio::Tools::Run::Simprot" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Simprot" --- # Bio::Tools::Run::Simprot(3pm) Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree ## NAME Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree ## 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) = $simprot->run(); ``` ## DESCRIPTION This is a wrapper around the Simprot program by Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier. Simprot allows for several models of amino acid substitution (PAM, JTT and PMB), allows for gamma distributed sites rates according to Yang's model, and implements a parameterised Qian and Goldstein distribution model for insertion and deletion. See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more information. ### Helping the module find your executable You will need to enable SIMPROTDIR to find the simprot program. This can be done in (at least) three ways: ``` 1. Make sure the simprot executable is in your path (i.e. 'which simprot' returns a valid program 2. define an environmental variable SIMPROTDIR which points to a directory containing the 'simprot' app: In bash export SIMPROTDIR=/home/progs/simprot or In csh/tcsh setenv SIMPROTDIR /home/progs/simprot 3. include a definition of an environmental variable SIMPROTDIR in every script that will BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; } use Bio::Tools::Run::Simprot; ``` ## 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. ``` 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. ### 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/ ``` ## AUTHOR - Albert Vilella Email avilella-at-gmail-dot-com ## 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 : ``` ### 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 object, L 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 object [optional] Args : L object L 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 object Returns : L object Args : [optional] L Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L ``` ### tree ``` Title : tree Usage : $simprot->tree($tree, %params); Function: Get/Set the L object Returns : L Args : [optional] $tree => L, [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::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 object Returns : L Args : none ```