# $Id: PhyloFit.pm 15196 2008-12-17 08:19:17Z sendu $ # # BioPerl module for Bio::Tools::Run::Phylo::Phast::PhyloFit # # Cared for by Sendu Bala <bix@sendu.me.uk> # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit =head1 SYNOPSIS 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); =head1 DESCRIPTION This is a wrapper for running the phyloFit application by Adam Siepel. You can get details here: http://compgen.bscb.cornell.edu/~acs/software.html Currently the interface is extremely simplified. Only the --tree form of usage is allowed (not --init-model), which means a tree must be supplied with the alignment (to run()). You can try supplying normal phyloFit arguments to new(), or calling arg-named methods (excluding initial hyphens and converting others to underscores, eg. $factory-E<gt>gaps_as_bases(1) to set the --gaps-as-bases arg). WARNING: the API may change in the future to allow for greater flexability and access to more phyloFit features. 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; =head1 FEEDBACK =head2 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 =head2 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://bugzilla.open-bio.org/ =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Run::Phylo::Phast::PhyloFit; use strict; use Cwd; use File::Spec; use Bio::AlignIO; use Bio::TreeIO; use base qw(Bio::Tools::Run::Phylo::PhyloBase); our $PROGRAM_NAME = 'phyloFit'; our $PROGRAM_DIR = $ENV{'PHASTDIR'}; # methods and their synonyms from the phastCons args we support our %PARAMS = (subst_mod => 's', min_informative => 'I', precision => 'p', log => 'l', ancestor => 'A', nrates => 'k', alpha => 'a', rate_constants => 'K', features => 'g', catmap => 'c', do_cats => 'C', reverse_groups => 'R'); our %SWITCHES = (gaps_as_bases => 'G', quiet => 'q', EM => 'E', init_random => 'r', estimate_freqs => 'F', markov => 'N', non_overlapping => 'V'); # just to be explicit, args we don't support (yet) or we handle ourselves our %UNSUPPORTED = (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'); =head2 program_name Title : program_name Usage : $factory>program_name() Function: holds the program name Returns : string Args : None =cut sub program_name { return $PROGRAM_NAME; } =head2 program_dir Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns : string Args : None =cut sub program_dir { return $PROGRAM_DIR; } =head2 new Title : new Usage : $factory = Bio::Tools::Run::Phylo::Phast::PhyloFit->new() Function: creates a new PhyloFit factory Returns : Bio::Tools::Run::Phylo::Phast::PhyloFit Args : Most options understood by phastCons can be supplied as key => value pairs. Options that don't normally take a value should be given a value of 1. You can type the keys as you would on the command line (eg. '--gaps-as-bases' => 1) or with only a single hyphen to start and internal hyphens converted to underscores (eg. -gaps_as_bases => 1) to avoid having to quote the key. These options can NOT be used with this wrapper currently: msa_format / i out_root / o tree / t help / h lnl / L init_model / M scale_only / B scale_subtree / S no_freqs / f no_rates / n post_probs / P expected_subs / X expected_total_subs / Z column_probs / U windows / w windows_explicit / v =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_set_from_args(\@args, -methods => {(map { $_ => $PARAMS{$_} } keys %PARAMS), (map { $_ => $SWITCHES{$_} } keys %SWITCHES)}, -create => 1); return $self; } =head2 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, $db_taxonomy_object); Function: Runs phyloFit on an alignment. Returns : filename of init.mod file produced Args : The first argument represents an alignment, the second argument a species tree. The alignment can be provided as a multi-fasta format alignment filename, or a Bio::Align::AlignI complient object (eg. a Bio::SimpleAlign). The species tree can be provided as a newick format tree filename or a Bio::Tree::TreeI complient object. Alternatively a Bio::DB::Taxonomy object can be supplied, in which case the species tree will be generated by using the alignment sequence names as species names and looking for those in the supplied database. In all cases, the alignment sequence names must correspond to node ids in the species tree. Multi-word species names should be joined with underscores to form the sequence names, eg. Homo_sapiens =cut sub run { my ($self, $aln, $tree) = @_; ($aln && $tree) || $self->throw("alignment and tree must be supplied"); $self->_alignment($aln); $tree = $self->_tree($tree); $tree->force_binary; # adjust tree node ids to convert spaces to underscores (eg. if tree # generated from taxonomy) foreach my $node ($tree->get_leaf_nodes) { my $id = $node->id; $id =~ s/ /_/g; $node->id($id); } # check node and seq names match $self->_check_names; return $self->_run; } sub _run { my $self = shift; my $exe = $self->executable || return; # cd to a temp dir my $temp_dir = $self->tempdir; my $cwd = Cwd->cwd(); chdir($temp_dir) || $self->throw("Couldn't change to temp dir '$temp_dir'"); my $aln_file = $self->_write_alignment; my $tree_file = $self->_write_tree; #...phyloFit --tree "(human,(mouse,rat))" --msa-format FASTA --out-root init alignment.fa my $command = $exe.$self->_setparams($aln_file, $tree_file); $self->debug("phyloFit command = $command\n"); system($command) && $self->throw("phyloFit call ($command) crashed: $?"); # cd back again chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'"); return File::Spec->catfile($temp_dir, 'init.mod'); } =head2 _setparams Title : _setparams Usage : Internal function, not to be called directly Function: Creates a string of params to be used in the command string Returns : string of params Args : alignment and tree file names =cut sub _setparams { my ($self, $aln_file, $tree_file) = @_; my $param_string = ' --tree '.$tree_file; $param_string .= ' --msa-format FASTA'; $param_string .= ' --out-root init'; # --min-informative defaults to 50, but must not be greater than the number # of bases in the alignment my $aln = $self->_alignment; my $length = $aln->length; my $min_informative = $self->min_informative || 50; if ($length < $min_informative) { $self->min_informative($length); } $param_string .= $self->SUPER::_setparams(-params => [keys %PARAMS], -switches => [keys %SWITCHES], -double_dash => 1, -underscore_to_dash => 1); $param_string .= ' '.$aln_file; return $param_string; } 1;