SYNOPSIS
# see Bio::Tools::Phylo::PAML for example usage
use Bio::Tools::Phylo::PAML;
my $parser = Bio::Tools::Phylo::PAML->new
(-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 %input_params = $result->get_input_parameters;
my @basfreq = $result->get_codon_pos_basefreq;
my $MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix
my $NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix
# for AAML runs
my $AAmatrix = $result->get_AADistMatrix;
my $AAMLmatrix = $result->get_AAMLDistMatrix;
# if -dir contains an rst file get list of
# Bio::PrimarySeq ancestral state reconstructions of the sequences
my @rsts = $result->get_rst_seqs;
# if you want to print the changes on the tree
# this will print out the
# anc_aa => ANCESTRAL AMINO ACID
# anc_prob => ANCESTRAL AA PROBABILITY
# derived_aa => DERIVED AA
# derived_prob => DERIVE AA PROBABILITY (where appropriate - NA for extant/tip taxas)
# site => which codon site this in the alignment
@trees = $result->get_rst_trees;
for my $t ( @trees ) {
for my $node ( $t->get_nodes ) {
next unless $node->ancestor; # skip root node
my @changes = $node->get_tag_values('changes');
my $chgstr = '';
for my $c ( @changes ) {
for my $k ( sort keys %$c ) {
$chgstr .= "$k => $c->{$k} ";
}
$chgstr .= "\n\t";
}
printf "node:%s n=%s s=%s\n\t%s\n",
$node->id,
$node->get_tag_values('n'),
$node->get_tag_values('s'),
$chgstr;
}
}
# Persite probabilities
my $persite = $result->get_rst_persite;
# let's score site 1
$site = $persite->[2];
# so site 2, node 2 (extant node, node 2)
print $site->[2]->{'codon'}, ' ',$site->[2]->{'aa'},"\n";
# site 2, node 3
print $site->[3]->{'codon'}, ' ',$site->[3]->{'aa'}, "\n";
# ancestral node 9, codon, aa, marginal probabilities; Yang95 is listed as
# (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650) in PAML rst file.
print $site->[9]->{'codon'}, ' ',$site->[9]->{'aa'}, ' ', $site->[9]->{'prob'}, ' ',
$site->[9]->{'Yang95_aa'},' ', $site->[9]->{'Yang95_aa_prob'},"\n";
DESCRIPTION
This is a container object for PAML Results.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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 of the bugs and their resolution. Bug reports can be submitted via email or the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich, Aaron Mackey
Email jason-at-bioperl-dot-org Email amackey-at-virginia-dot-edu
CONTRIBUTORS
Albert Vilella avilella-AT-gmail-DOT-comAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : my $obj = Bio::Tools::Phylo::PAML::Result->new(%data);
Function: Builds a new Bio::Tools::Phylo::PAML::Result object
Returns : Bio::Tools::Phylo::PAML::Result
Args : -trees => array reference of Bio::Tree::TreeI objects
-MLmatrix => ML matrix
-seqs => array reference of 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)
-ntfreq => array ref of NT frequencies (only for BASEML)
-seqfile => seqfile used
-kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML)
-alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML)
-NSSitesresult => arrayref of PAML::ModelResult
-input_params => input params from .ctl file
-rst => array reference of Bio::PrimarySeqI objects
of ancestral state reconstruction
-rst_persite=> arrayref of persite data, this is a complicated set of AoH
-rst_trees => rst trees with changes coded on the tree
See Also: Bio::Tree::TreeI, Bio::PrimarySeqI, Bio::Matrix::PhylipDist, Bio::Tools::Phylo::PAML
next_tree
Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L<Bio::Tree::TreeI> Args : none
get_trees
Title : get_trees Usage : my @trees = $result->get_trees; Function: Get all the parsed trees as an array Returns : Array of trees Args : none
rewind_tree_iterator
Title : rewind_tree_iterator
Usage : $result->rewind_tree_iterator()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args : none
add_tree
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>
set_MLmatrix
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)
get_MLmatrix
Title : get_MLmatrix Usage : my $mat = $result->get_MLmatrix() Function: Get the ML matrix Returns : 2D Array reference Args : none
set_NGmatrix
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)
get_NGmatrix
Title : get_NGmatrix Usage : my $mat = $result->get_NGmatrix() Function: Get the Nei & Gojobori matrix Returns : 2D Array reference Args : none
add_seq
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>
reset_seqs
Title : reset_seqs Usage : $result->reset_seqs Function: Reset the OTU seqs stored Returns : none Args : none
get_seqs
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>
set_codon_pos_basefreq
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
get_codon_pos_basefreq
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
version
Title : version Usage : $obj->version($newval) Function: Get/Set version Returns : value of version Args : newvalue (optional)
seqfile
Title : seqfile Usage : $obj->seqfile($newval) Function: Get/Set seqfile Returns : value of seqfile Args : newvalue (optional)
model
Title : model Usage : $obj->model($newval) Function: Get/Set model Returns : value of model Args : on set, new value (a scalar or undef, optional)
patterns
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
: }
set_AAFreqs
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
get_AAFreqs
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
set_NTFreqs
Title : set_NTFreqs
Usage : $result->set_NTFreqs(\%aafreqs);
Function: Get/Set NT 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
get_NTFreqs
Title : get_NTFreqs
Usage : my %all_nt_freqs = $result->get_NTFreqs()
OR
my %seq_nt_freqs = $result->get_NTFreqs($seqname)
Function: Get the NT freqs, either for every sequence or just
for a specific sequence
The average nt freqs for the entire set are also available
for the sequence named 'Average'
Returns : Hashref
Args : (optional) sequence name to retrieve nt freqs for
add_stat
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
get_stat
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
get_stat_names
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
get_AADistMatrix
Title : get_AADistMatrix Usage : my $mat = $obj->get_AADistMatrix() Function: Get AADistance Matrix Returns : value of AADistMatrix (Bio::Matrix::PhylipDist) Args : none
set_AADistMatrix
Title : set_AADistMatrix Usage : $obj->set_AADistMatrix($mat); Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AADistrance Matrix (Bio::Matrix::PhylipDist)
get_AAMLDistMatrix
Title : get_AAMLDistMatrix Usage : my $mat = $obj->get_AAMLDistMatrix() Function: Get AAMLDistance Matrix Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist) Args : none
set_AAMLDistMatrix
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)
add_NSSite_result
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
get_NSSite_results
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
set_CodonFreqs
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)
get_CodonFreqs
Title : get_CodonFreqs Usage : my @codon_freqs = $result->get_CodonFreqs() Function: Get the Codon freqs Returns : Array Args : none
BASEML Relavent values
get_KappaMatrix
Title : get_KappaMatrix Usage : my $mat = $obj->get_KappaMatrix() Function: Get KappaDistance Matrix Returns : value of KappaMatrix (Bio::Matrix::PhylipDist) Args : none
set_KappaMatrix
Title : set_KappaMatrix Usage : $obj->set_KappaMatrix($mat); Function: Set the KappaDistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : KappaDistrance Matrix (Bio::Matrix::PhylipDist)
get_AlphaMatrix
Title : get_AlphaMatrix Usage : my $mat = $obj->get_AlphaMatrix() Function: Get AlphaDistance Matrix Returns : value of AlphaMatrix (Bio::Matrix::PhylipDist) Args : none
set_AlphaMatrix
Title : set_AlphaMatrix Usage : $obj->set_AlphaMatrix($mat); Function: Set the AlphaDistrance Matrix (Bio::Matrix::PhylipDist) Returns : none Args : AlphaDistrance Matrix (Bio::Matrix::PhylipDist)
set_input_parameter
Title : set_input_parameter Usage : $obj->set_input_parameter($p,$vl); Function: Set an Input Parameter Returns : none Args : $parameter and $value
get_input_parameters
Title : get_input_parameters Usage : $obj->get_input_parameters; Function: Get Input Parameters Returns : Hash of key/value pairs Args : none
reset_input_parameters
Title : reset_input_parameters Usage : $obj->reset_input_parameters; Function: Reset the Input Parameters hash Returns : none Args : none
Reconstructed Ancestral State relevant options
add_rst_seq
Title : add_rst_seq Usage : $obj->add_rst_seq($seq) Function: Add a Bio::PrimarySeq to the RST Result Returns : none Args : Bio::PrimarySeqI See also : L<Bio::PrimarySeqI>
reset_rst_seqs
Title : reset_rst_seqs Usage : $result->reset_rst_seqs Function: Reset the RST seqs stored Returns : none Args : none
get_rst_seqs
Title : get_rst_seqs Usage : my @otus = $result->get_rst_seqs Function: Get the seqs Bio::PrimarySeq Returns : Array of Bio::PrimarySeqI objects Args : None See also : L<Bio::PrimarySeq>
add_rst_tree
Title : add_rst_tree Usage : $obj->add_rst_tree($tree) Function: Add a Bio::Tree::TreeI to the RST Result Returns : none Args : Bio::Tree::TreeI See also : L<Bio::Tree::TreeI>
reset_rst_trees
Title : reset_rst_trees Usage : $result->reset_rst_trees Function: Reset the RST trees stored Returns : none Args : none
get_rst_trees
Title : get_rst_trees Usage : my @otus = $result->get_rst_trees Function: Get the trees Bio::Tree::TreeI Returns : Array of Bio::Tree::TreeI objects Args : None See also : L<Bio::Tree::TreeI>
set_rst_persite
Title : set_rst_persite Usage : $obj->set_rst_persite($newval) Function: Get/Set the per-site RST values Returns : value of set_rst_persite (a scalar) Args : on set, new value (a scalar or undef, optional)
get_rst_persite
Title : get_rst_persite
Usage : my @rst_persite = @{$result->get_rst_persite()}
Function: Get the per-site RST values
Returns : Array
Args : none