Bio::Tools::Phylo::PAML::Result - A PAML result set object
# see Bio::Tools::Phylo::PAML for example usage use Bio::Tools::Phylo::PAML; my $parser = new Bio::Tools::Phylo::PAML (-file => "./results/mlc", -dir => "./results/"); # get the first/next result; a Bio::Tools::Phylo::PAML::Result object, # which isa Bio::SeqAnalysisResultI object. my $result = $parser->next_result(); my @seqs = $result->get_seqs; my @MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix my @NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix my @basfreq = $result->get_codon_pos_basefreq;
This is a container object for PAML Results.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Tools::Phylo::PAML::Result(%data); Function: Builds a new Bio::Tools::Phylo::PAML::Result object Returns : Bio::Tools::Phylo::PAML::Result Args : -trees => array reference of L<Bio::Tree::TreeI> objects -MLmatrix => ML matrix -seqs => array reference of L<Bio::PrimarySeqI> objects -codonpos => array reference of codon positions -codonfreq => array reference of codon frequencies -version => version string -model => model string -patterns => hashref with the fields '-patterns', '-ns', '-ls' -stats => array ref of misc stats (optional) -aafreq => Hashref of AA frequencies (only for AAML) -aadistmat => Bio::Matrix::PhylipDist (only for AAML) -aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML) -NSSitesresult => arrayref of PAML::ModelResult
Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L<Bio::Tree::TreeI> Args : none
Title : get_trees Usage : my @trees = $result->get_trees; Function: Get all the parsed trees as an array Returns : Array of trees Args : none
Title : rewind_tree_iterator Usage : $result->rewind_tree() Function: Rewinds the tree iterator so that next_tree can be called again from the beginning Returns : none Args : none
Title : add_tree Usage : $result->add_tree($tree); Function: Adds a tree Returns : integer which is the number of trees stored Args : L<Bio::Tree::TreeI>
Title : set_MLmatrix Usage : $result->set_MLmatrix($mat) Function: Set the ML Matrix Returns : none Args : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise)
Title : get_MLmatrix Usage : my $mat = $result->get_MLmatrix() Function: Get the ML matrix Returns : 2D Array reference Args : none
Title : set_NGmatrix Usage : $result->set_NGmatrix($mat) Function: Set the Nei & Gojobori Matrix Returns : none Args : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise)
Title : get_NGmatrix Usage : my $mat = $result->get_NGmatrix() Function: Get the Nei & Gojobori matrix Returns : 2D Array reference Args : none
Title : add_seq Usage : $obj->add_seq($seq) Function: Add a Bio::PrimarySeq to the Result Returns : none Args : Bio::PrimarySeqI See also : L<Bio::PrimarySeqI>
Title : reset_seqs Usage : $result->reset_seqs Function: Reset the OTU seqs stored Returns : none Args : none
Title : get_seqs Usage : my @otus = $result->get_seqs Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit) Returns : Array of Bio::PrimarySeq Args : None See also : L<Bio::PrimarySeq>
Title : set_codon_pos_basefreq Usage : $result->set_codon_pos_basefreq(@freqs) Function: Set the codon position base frequencies Returns : none Args : Array of length 3 where each slot has a hashref keyed on DNA base
Title : get_codon_pos_basefreq Usage : my @basepos = $result->get_codon_pos_basefreq; Function: Get the codon position base frequencies Returns : Array of length 3 (each codon position), each slot is a hashref keyed on DNA bases, the values are the frequency of the base at that position for all sequences Args : none Note : The array starts at 0 so position '1' is in position '0' of the array
Title : version Usage : $obj->version($newval) Function: Get/Set version Returns : value of version Args : newvalue (optional)
Title : model Usage : $obj->model($newval) Function: Get/Set model Returns : value of model Args : on set, new value (a scalar or undef, optional)
Title : patterns Usage : $obj->patterns($newval) Function: Get/Set Patterns hash Returns : Hashref of pattern data Args : [optional] Hashref of patterns : The hashref is typically : { -patterns => \@arrayref : -ns => $ns : -ls => $ls : }
Title : set_AAFreqs Usage : $result->set_AAFreqs(\%aafreqs); Function: Get/Set AA freqs Returns : none Args : Hashref, keys are the sequence names, each points to a hashref which in turn has keys which are the amino acids
Title : get_AAFreqs Usage : my %all_aa_freqs = $result->get_AAFreqs() OR my %seq_aa_freqs = $result->get_AAFreqs($seqname) Function: Get the AA freqs, either for every sequence or just for a specific sequence The average aa freqs for the entire set are also available for the sequence named 'Average' Returns : Hashref Args : (optional) sequence name to retrieve aa freqs for
Title : add_stat Usage : $result->add_stat($stat,$value); Function: Add some misc stat valuess (key/value pairs) Returns : none Args : $stat stat name $value stat value
Title : get_stat Usage : my $value = $result->get_stat($name); Function: Get the value for a stat of a given name Returns : scalar value Args : name of the stat
Title : get_stat_names Usage : my @names = $result->get_stat_names; Function: Get the stat names stored for the result Returns : array of names Args : none
Title : get_AADistMatrix Usage : my $mat = $obj->get_AADistMatrix() Function: Get AADistance Matrix Returns : value of AADistMatrix (Bio::Matrix::PhylipDist) Args : none
Title : set_AADistMatrix Usage : $obj->set_AADistMatrix($mat); Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AADistrance Matrix (Bio::Matrix::PhylipDist)
Title : get_AAMLDistMatrix Usage : my $mat = $obj->get_AAMLDistMatrix() Function: Get AAMLDistance Matrix Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist) Args : none
Title : set_AAMLDistMatrix Usage : $obj->set_AAMLDistMatrix($mat); Function: Set the AA ML Distrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AAMLDistrance Matrix (Bio::Matrix::PhylipDist)
Title : add_NSSite_result Usage : $result->add_NSSite_result($model) Function: Add a NSsite result (PAML::ModelResult) Returns : none Args : Bio::Tools::Phylo::PAML::ModelResult
Title : get_NSSite_results Usage : my @results = @{$self->get_NSSite_results}; Function: Get the reference to the array of NSSite_results Returns : Array of PAML::ModelResult results Args : none
Title : set_CodonFreqs Usage : $obj->set_CodonFreqs($newval) Function: Get/Set the Codon Frequence table Returns : value of set_CodonFreqs (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : get_CodonFreqs Usage : my @codon_freqs = $result->get_CodonFreqs() Function: Get the Codon freqs Returns : Array Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.