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

📦
version 1.7.3 · 3 versions
, in debian bookworm, debian trixie

🌸 NAME 🌸

okay so bestie, this is the manual page for Bio::Tools::Phylo::PAML::Result(3pm) 💖

Bio::Tools::Phylo::PAML::Result — it's a PAML result set object, no cap 🧬✨

👑 VERSION 👑

version 1.7.3 🫶

✨ SYNOPSIS ✨

like, here's the vibe in code form, fr fr:

# 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 💖

okay so basically? This is a container object for PAML Results 🫙✨ It just holds all the lil result goodies for you so you don't have to go digging around in files yourself. iconic behaviour honestly.

🎀 METHODS 🎀

🧚 new

  • Title — new
  • Usage — my $obj = Bio::Tools::Phylo::PAML::Result->new(%data);
  • Function — builds a brand new Bio::Tools::Phylo::PAML::Result object, slay 💅
  • Returns — Bio::Tools::Phylo::PAML::Result
  • Args — here's the whole menu, no skips:
    • -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 — grabs the next tree off the factory, one at a time bestie
  • Returns — Bio::Tree::TreeI
  • Args — none

🌳 get_trees

  • Title — get_trees
  • Usage — my @trees = $result->get_trees;
  • Function — get every single parsed tree, 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 you can call next_tree all over again from the very beginning, like a rewatch 🔁
  • Returns — none
  • Args — none

🍓 add_tree

  • Title — add_tree
  • Usage — $result->add_tree($tree);
  • Function — adds a tree, one more for the collection
  • Returns — integer, which is literally the number of trees stored
  • Args — Bio::Tree::TreeI

👑 set_MLmatrix

  • Title — set_MLmatrix
  • Usage — $result->set_MLmatrix($mat)
  • Function — sets the ML Matrix
  • Returns — none
  • Args — Arrayref to MLmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise)
ngl the original says "whic" and I'm keeping it, I don't make the rules 💀

✨ get_MLmatrix

  • Title — get_MLmatrix
  • Usage — my $mat = $result->get_MLmatrix()
  • Function — gets the ML matrix
  • Returns — 2D Array reference
  • Args — none

💜 set_NGmatrix

  • Title — set_NGmatrix
  • Usage — $result->set_NGmatrix($mat)
  • Function — sets 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 — gets the Nei & Gojobori matrix
  • Returns — 2D Array reference
  • Args — none

🧬 add_seq

  • Title — add_seq
  • Usage — $obj->add_seq($seq)
  • Function — adds a Bio::PrimarySeq to the Result
  • Returns — none
  • Args — Bio::PrimarySeqI
  • See also — Bio::PrimarySeqI

🎀 reset_seqs

  • Title — reset_seqs
  • Usage — $result->reset_seqs
  • Function — resets all the OTU seqs that were stored, clean slate energy ✨
  • Returns — none
  • Args — none

🌸 get_seqs

  • Title — get_seqs
  • Usage — my @otus = $result->get_seqs
  • Function — gets the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit) — yep, that's what OTU means, iykyk
  • Returns — Array of Bio::PrimarySeq
  • Args — None
  • See also — Bio::PrimarySeq

💅 set_codon_pos_basefreq

  • Title — set_codon_pos_basefreq
  • Usage — $result->set_codon_pos_basefreq(@freqs)
  • Function — sets 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 — gets 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. yes this is off-by-one, yes you have to deal with it 🙈

🫶 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 — gets the AA freqs, either for every single sequence or just for one specific sequence 💅 The average aa freqs for the entire set are also available, under the sequence named 'Average' — cute right?
  • 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 — gets the NT freqs, either for every single sequence or just for one specific one ✨ The average nt freqs for the entire set are also available under 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 — adds some misc stat valuess (key/value pairs)
bestie the original really did spell it "valuess" and I'm not about to gaslight you about it 😭
  • Returns — none
  • Args — $stat = stat name, $value = stat value

⭐ get_stat

  • Title — get_stat
  • Usage — my $value = $result->get_stat($name);
  • Function — gets 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 — gets all the stat names that got stored for the result
  • Returns — array of names
  • Args — none

💫 get_AADistMatrix

  • Title — get_AADistMatrix
  • Usage — my $mat = $obj->get_AADistMatrix()
  • Function — gets the AADistance Matrix
  • Returns — value of AADistMatrix (Bio::Matrix::PhylipDist)
  • Args — none

set_AADistMatrix ✨

  • Title: set_AADistMatrix
  • Usage: $obj->set_AADistMatrix($mat);
  • Function: plugs in the AADistrance Matrix (Bio::Matrix::PhylipDist)
  • Returns: nothing, babes — it's a setter
  • Args: AADistrance Matrix (Bio::Matrix::PhylipDist)

get_AAMLDistMatrix 💖

  • Title: get_AAMLDistMatrix
  • Usage: my $mat = $obj->get_AAMLDistMatrix()
  • Function: hands you the AAML Distance Matrix
  • Returns: the value of AAMLDistMatrix (Bio::Matrix::PhylipDist)
  • Args: none

set_AAMLDistMatrix 🎀

  • Title: set_AAMLDistMatrix
  • Usage: $obj->set_AAMLDistMatrix($mat);
  • Function: sets the AA ML Distrance Matrix (Bio::Matrix::PhylipDist)
  • Returns: none
  • Args: AAML Distrance Matrix (Bio::Matrix::PhylipDist)

add_NSSite_result 🦋

  • Title: add_NSSite_result
  • Usage: $result->add_NSSite_result($model)
  • Function: adds one 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: gives you back the reference to the array of NSSite_results
  • Returns: an Array of PAML::ModelResult results
  • Args: none

set_CodonFreqs 💅

  • Title: set_CodonFreqs
  • Usage: $obj->set_CodonFreqs($newval)
  • Function: get/set the Codon Frequence table (that's literally how the doc spells it, and honestly? iconic)
  • Returns: the value of set_CodonFreqs (a scalar)
  • Args: on set, the new value (a scalar or undef, optional)

get_CodonFreqs 🍓

  • Title: get_CodonFreqs
  • Usage: my @codon_freqs = $result->get_CodonFreqs()
  • Function: grabs the Codon freqs
  • Returns: Array
  • Args: none

get_KappaMatrix 🔥

  • Title: get_KappaMatrix
  • Usage: my $mat = $obj->get_KappaMatrix()
  • Function: gets you the KappaDistance Matrix
  • Returns: the value of KappaMatrix (Bio::Matrix::PhylipDist)
  • Args: none

set_KappaMatrix 💜

  • Title: set_KappaMatrix
  • Usage: $obj->set_KappaMatrix($mat);
  • Function: sets 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: gets you the AlphaDistance Matrix
  • Returns: the value of AlphaMatrix (Bio::Matrix::PhylipDist)
  • Args: none

set_AlphaMatrix ⭐

  • Title: set_AlphaMatrix
  • Usage: $obj->set_AlphaMatrix($mat);
  • Function: sets 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: sets one input parameter
  • Returns: none
  • Args: $parameter and $value

get_input_parameters 👑

  • Title: get_input_parameters
  • Usage: $obj->get_input_parameters;
  • Function: gets the input parameters
  • Returns: a Hash of key/value pairs
  • Args: none

reset_input_parameters 🧚

  • Title: reset_input_parameters
  • Usage: $obj->reset_input_parameters;
  • Function: wipes the input parameters hash clean, fresh start energy
  • Returns: none
  • Args: none

add_rst_seq 🌸

  • Title: add_rst_seq
  • Usage: $obj->add_rst_seq($seq)
  • Function: adds 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: resets the RST seqs that were being stored
  • Returns: none
  • Args: none

get_rst_seqs 🦋

  • Title: get_rst_seqs
  • Usage: my @otus = $result->get_rst_seqs
  • Function: gets the seqs, Bio::PrimarySeq
  • Returns: an 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: adds 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: resets the RST trees that were hanging around in there
  • Returns: none
  • Args: none

get_rst_trees 💜

  • Title: get_rst_trees
  • Usage: my @otus = $result->get_rst_trees
  • Function: gets the trees, Bio::Tree::TreeI
  • Returns: an 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: the value of set_rst_persite (a scalar)
  • Args: on set, the new value (a scalar or undef, optional)

get_rst_persite 🍓

  • Title: get_rst_persite
  • Usage: my @rst_persite = @{$result->get_rst_persite()}
  • Function: gets the per-site RST values
  • Returns: Array
  • Args: none

🌿 Reconstructed Ancestral State relevant options 🌿

Just dropping it here, no notes.

💬 FEEDBACK 💬

Mailing lists 📬

Your feedback is like, genuinely load-bearing for the evolution of this module and every other Bioperl module out there. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is so appreciated, fr fr.

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/Support.html    - About the mailing lists

Support 🫶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…rather than going straight to the module maintainer, bestie. There are lots of experienced and responsive experts who'll look at the problem and get back to you quickly. And if it's at all possible, include a thorough description of the problem with code and data examples. No vibes-only bug reports, please and thank you.

Reporting bugs 🐛

Report bugs to the Bioperl bug tracking system so we can actually keep track of the bugs and their resolutions — very demure, very mindful of us.

Bug reports can be submitted via the web:

https://github.com/bioperl/bio-tools-phylo-paml/issues

👑 AUTHORS 👑

  • Jason Stajich <jason@bioperl.org>
  • Aaron Mackey <amackey@virginia.edu>
  • Albert Vilella <avilella@gmail.com>

This software is copyright (c) by Jason Stajich <jason@bioperl.org>, and by Aaron Mackey <amackey@virginia.edu>.

This software is available under the same terms as the perl 5 programming language system itself.

And that's the whole page, bestie — perl v5.34.0, dated 2022-10-14, straight from the Bio::T...:Result(3pm) manpage. Go read the source, it's giving main character energy 💅✨

📦 where this page comes from