Bio::Tools::Phylo PAML
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Summary
Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml,
baseml, basemlg, codemlsites and yn00
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Bio::Matrix::PhylipDist
Bio::PrimarySeq
Bio::Tools::Phylo::PAML::ModelResult
Bio::Tools::Phylo::PAML::Result
Bio::TreeIO
File::Spec
IO::String
Inherit
Bio::AnalysisParserI Bio::Root::IO Bio::Root::Root
Synopsis
  #!/usr/bin/perl -Tw
use strict;
use Bio::Tools::Phylo::PAML; # need to specify the output file name (or a fh) (defaults to # -file => "codeml.mlc"); also, optionally, the directory in which # the other result files (rst, 2ML.dS, etc) may be found (defaults # to "./") 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(); # get the sequences used in the analysis; returns Bio::PrimarySeq # objects (OTU = Operational Taxonomic Unit). my @otus = $result->get_seqs(); # codon summary: codon usage of each sequence [ arrayref of { # hashref of counts for each codon } for each sequence and the # overall sum ], and positional nucleotide distribution [ arrayref # of { hashref of frequencies for each nucleotide } for each # sequence and overall frequencies ]: my ($codonusage, $ntdist) = $result->get_codon_summary(); # example manipulations of $codonusage and $ntdist: printf "There were %d %s codons in the first seq (%s)\n", $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id(); printf "There were %d %s codons used in all the sequences\n", $codonusage->[$#{$codonusage}]->{AAA}, 'AAA'; printf "Nucleotide %c was present %g of the time in seq %s\n", 'A', $ntdist->[1]->{A}, $otus[1]->id(); # get Nei & Gojobori dN/dS matrix: my $NGmatrix = $result->get_NGmatrix(); # get ML-estimated dN/dS matrix, if calculated; this corresponds to # the runmode = -2, pairwise comparison usage of codeml my $MLmatrix = $result->get_MLmatrix(); # These matrices are length(@otu) x length(@otu) "strict lower # triangle" 2D-matrices, which means that the diagonal and # everything above it is undefined. Each of the defined cells is a # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", # "S" and "N". If a ML matrix, "lnL" and "kappa" will also be defined. printf "The omega ratio for sequences %s vs %s was: %g\n", $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega}; # with a little work, these matrices could also be passed to # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building # method that accepts a matrix of "distances" (using the LOWTRI # option): my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ]; # for runmode's other than -2, get tree topology with estimated # branch lengths; returns a Bio::Tree::TreeI-based tree object with # added PAML parameters at each node my ($tree) = $result->get_trees(); for my $node ($tree->get_nodes()) { # inspect the tree: the "t" (time) parameter is available via # $node->branch_length(); all other branch-specific parameters # ("omega", "dN", etc.) are available via # ($omega) = $node->get_tag_values('omega'); } # if you are using model based Codeml then trees are stored in each # modelresult object for my $modelresult ( $result->get_NSSite_results ) { # model M0, M1, etc print "model is ", $modelresult->model_num, "\n"; my ($tree) = $modelresult->get_trees(); for my $node ($tree->get_nodes()) { # inspect the tree: the "t" (time) parameter is available via # $node->branch_length(); all other branch-specific parameters # ("omega", "dN", etc.) are available via # ($omega) = $node->get_tag_values('omega'); } } # get any general model parameters: kappa (the # transition/transversion ratio), NSsites model parameters ("p0", # "p1", "w0", "w1", etc.), etc. my $params = $result->get_model_params(); printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1}; # parse AAML result files my $aamat = $result->get_AADistMatrix(); my $aaMLmat = $result->get_AAMLDistMatrix();
Description
This module is used to parse the output from the PAML programs codeml,
baseml, basemlg, codemlsites and yn00. You can use the
Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the
PAML programs, but this module is only useful to parse the output.
This module has fledgling support for PAML version 4.3a (October 2009).
Please report any problems to the mailing list (see FEEDBACK below).
Methods
BEGIN Code
newDescriptionCode
next_resultDescriptionCode
_parse_summary
No description
Code
_parse_inputparams
No description
Code
_parse_codon_freqs
No description
Code
_parse_aa_freqs
No description
Code
_parse_StarDecomposition
No description
Code
_parse_aa_dists
No description
Code
_parse_patterns
No description
Code
_parse_seqs
No description
Code
_parse_distmat
No description
Code
_parse_PairwiseCodon
No description
Code
_parse_YN_Pairwise
No description
Code
_parse_Forestry
No description
Code
_parse_NSsitesBatch
No description
Code
_parse_Pos_selected_sites
No description
Code
_parse_branch_dnds
No description
Code
_parse_nt_freqs
No description
Code
_parse_nt_dists
No description
Code
_parse_rate_parametes
No description
Code
_parse_rst
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Phylo::PAML->new(%args);
Function: Builds a new Bio::Tools::Phylo::PAML object
Returns : Bio::Tools::Phylo::PAML
Args : Hash of options: -file, -fh, -dir
-file (or -fh) should contain the contents of the PAML
outfile;
-dir is the (optional) name of the directory in
which the PAML program was run (and includes other
PAML-generated files from which we can try to gather data)
next_resultcodeprevnextTop
 Title   : next_result
Usage : $result = $obj->next_result();
Function: Returns the next result available from the input, or
undef if there are no more results.
Example :
Returns : a Bio::Tools::Phylo::PAML::Result object
Args : none
Methods code
BEGINTop
BEGIN {
    $RSTFILENAME = 'rst';    # where to get the RST data from
}
newdescriptionprevnextTop
sub new {
    my ( $class, @args ) = @_;

    my $self = $class->SUPER::new(@args);
    $self->_initialize_io(@args);
    my ($dir) = $self->_rearrange( [qw(DIR)], @args );
    $self->{_dir} = $dir if defined $dir;
    return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    my %data;

    # parse the RST file, if it doesn't exist or if dir is not set
# this will just skip the parsing
$self->_parse_rst(); my $idlookup; # a hashreference to SEQID (number) ==> 'SEQUENCENAME'
# get the various codon and other sequence summary data, if necessary:
$self->_parse_summary unless ( $self->{'_summary'} && !$self->{'_summary'}->{'multidata'} ); # OK, depending on seqtype and runmode now, one of a few things can happen:
my $seqtype = $self->{'_summary'}->{'seqtype'}; if ( $seqtype eq 'CODONML' || $seqtype eq 'AAML' ) { my $has_model_line = 0; while ( defined( $_ = $self->_readline ) ) { if ( $seqtype eq 'CODONML' && m/^pairwise comparison, codon frequencies:/ )
{

# runmode = -2, CODONML
$self->debug("pairwise Ka/Ks\n");
$self->_pushback($_); %data = $self->_parse_PairwiseCodon; last; } elsif ( $seqtype eq 'AAML' && m/^ML distances of aa seqs\.$/ ) {
$self->_pushback($_);
# get AA distances
%data = ( '-AAMLdistmat' => $self->_parse_aa_dists() ); # $self->_pushback($_);
# %data = $self->_parse_PairwiseAA;
# last;
} elsif ( m/^Model\s+(\d+)/
|| ( ( !
$has_model_line && m/^TREE/ )
&&
$seqtype eq 'CODONML'
&& (
$self->{'_summary'}->{'version'} !~ /4/))
# last bit to keep PAML >= 4 from being caught here
# bug 2482. Not sure this is the right fix, but tests
# pass and the bug's test case passes.
)
{
$self->_pushback($_);
my $model = $self->_parse_NSsitesBatch; push @{ $data{'-NSsitesresults'} }, $model; $has_model_line = 1; } elsif (m/for each branch/) {
my
%branch_dnds = $self->_parse_branch_dnds;
if ( !defined $data{'-trees'} ) { $self->warn( "No trees have been loaded, can't do anything\n"); next; } my ($tree) = @{ $data{'-trees'} }; if ( !$tree || !ref($tree) || !$tree->isa('Bio::Tree::Tree') ) { $self->warn("no tree object already stored!\n"); next; } # These need to be added to the Node/branches
while ( my ( $k, $v ) = each %branch_dnds ) { # we can probably do better by caching at some point
my @nodes; for my $id ( split( /\.\./, $k ) ) { my @nodes_L = map { $tree->find_node( -id => $_ ) } @{ $idlookup->{$id} }; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn("no node for $n\n"); } unless ( $n->is_Leaf && $n->id ) { $n->id($id); } push @nodes, $n; } my ( $parent, $child ) = @nodes; while ( my ( $kk, $vv ) = each %$v ) { $child->add_tag_value( $kk, $vv ); } } } elsif (m/^TREE/) {

# runmode = 0
$self->_pushback($_);
( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; #last;
} elsif (m/Heuristic tree search by stepwise addition$/) {

# runmode = 3
$self->throw(
-class => 'Bio::Root::NotImplemented',
-text => "StepwiseAddition not yet implemented!"
);
# $self->_pushback($_);
# %data = $self->_parse_StepwiseAddition;
# last;
} elsif (m/Heuristic tree search by NNI perturbation$/) {

# runmode = 4
$self->throw(
-class => 'Bio::Root::NotImplemented',
-text => "NNI Perturbation not yet implemented!"
);
# $self->_pushback($_);
# %data = $self->_parse_Perturbation;
# last;
} elsif (m/^stage 0:/) {

# runmode = (1 or 2)
$self->throw(
-class => 'Bio::Root::NotImplemented',
-text => "StarDecomposition not yet implemented!"
);
$self->_pushback($_); %data = $self->_parse_StarDecomposition; last; } } } elsif ( $seqtype eq 'BASEML' ) { while ( defined( $_ = $self->_readline ) ) { if (/^Distances:/) { $self->_pushback($_); my ( $kappa, $alpha ) = $self->_parse_nt_dists(); %data = ( '-kappa_distmat' => $kappa, '-alpha_distmat' => $alpha ); } elsif (/^TREE/) { $self->_pushback($_); ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; } } } elsif ( $seqtype eq 'YN00' ) { while ( $_ = $self->_readline ) { if ( m/^Estimation by the method|\(B\) Yang & Nielsen \(2000\) method/
)
{
$self->_pushback($_);
%data = $self->_parse_YN_Pairwise; last; } } } if (%data) { $data{'-version'} = $self->{'_summary'}->{'version'}; $data{'-seqs'} = $self->{'_summary'}->{'seqs'}; $data{'-patterns'} = $self->{'_summary'}->{'patterns'}; $data{'-ngmatrix'} = $self->{'_summary'}->{'ngmatrix'}; $data{'-codonpos'} = $self->{'_summary'}->{'codonposition'}; $data{'-codonfreq'} = $self->{'_summary'}->{'codonfreqs'}; $data{'-model'} = $self->{'_summary'}->{'model'}; $data{'-seqfile'} = $self->{'_summary'}->{'seqfile'}; $data{'-aadistmat'} = $self->{'_summary'}->{'aadistmat'}; $data{'-stats'} = $self->{'_summary'}->{'stats'}; $data{'-aafreq'} = $self->{'_summary'}->{'aafreqs'}; $data{'-ntfreq'} = $self->{'_summary'}->{'ntfreqs'}; $data{'-input_params'} = $self->{'_summary'}->{'inputparams'}; $data{'-rst'} = $self->{'_rst'}->{'rctrted_seqs'}; $data{'-rst_persite'} = $self->{'_rst'}->{'persite'}; $data{'-rst_trees'} = $self->{'_rst'}->{'trees'}; return Bio::Tools::Phylo::PAML::Result->new(%data); } else { return; }
}
_parse_summarydescriptionprevnextTop
sub _parse_summary {
    my ($self) = @_;

    # Depending on whether verbose > 0 or not, and whether the result
# set comes from a multi-data run, the first few lines could be
# various things; we're going to throw away any sequence data
# here, since we'll get it later anyways
# multidata ? : \n\nData set 1\n
# verbose ? : cleandata ? : \nBefore deleting alignment gaps. \d sites\n
# [ sequence printout ]
# \nAfter deleting gaps. \d sites\n"
# : [ sequence printout ]
# CODONML (in paml 3.12 February 2002) <<-- what we want to see!
my $SEQTYPES = qr( (?: (?: CODON | AA | BASE | CODON2AA ) ML ) | YN00 )x; my $line; $self->{'_already_parsed_seqs'} = $self->{'_already_parsed_seqs'} ? 1 : 0; my @lines; while ( $_ = $self->_readline ) { push @lines, $_; if (m/^($SEQTYPES) \s+ # seqtype: CODONML, AAML, BASEML, CODON2AAML, YN00, etc
(?: \(in \s+ ([^\)]+?) \s* \) \s* )? # version: "paml 3.12 February 2002"; not present < 3.1 or YN00
(\S+) \s* # tree filename
(?: (.+?) )? # model description (not there in YN00)
\s* $ # trim any trailing space
/ox
)
{
@{ $self->{'_summary'} }{qw(seqtype version seqfile model)} =
( $1, $2, $3, $4 );
# in 4.3, the model is on its own line
if ( !defined $self->{'_summary'}->{'model'} ) { my $model_line = $self->_readline; chomp $model_line; if ($model_line =~ /^Model:/) { $self->{'_summary'}->{'model'} = $model_line; } } defined $self->{'_summary'}->{'model'} && $self->{'_summary'}->{'model'} =~ s/Model:\s+//; $self->_pushback($_) if $self->{'_summary'}->{'seqtype'} eq 'AAMODEL'; last; } elsif ((m/\s+?\d+?\s+?\d+?/) && ( $self->{'_already_parsed_seqs'} != 1 )) {
$self->_parse_seqs;
} elsif (m/^Data set \d$/) {
$self->{'_summary'} = {};
$self->{'_summary'}->{'multidata'}++; } elsif (m/^Before\s+deleting\s+alignment\s+gaps/) { #Gap
my (
$phylip_header) = $self->_readline;
$self->_parse_seqs; } elsif ( ( @lines >= 3 ) && ( $self->{'_already_parsed_seqs'} != 1 ) ) { #No gap
# don't start parsing seqs yet if we're on a blank line
# (gives another opportunity to match one of the other regexes)
unless (/^\n$/) { $self->_parse_seqs; } } elsif ( (/Printing out site pattern counts/) && ( $self->{'_already_parsed_seqs'} != 1 ) ) { $self->_parse_patterns; } } unless ( defined $self->{'_summary'}->{'seqtype'} ) { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'Unknown format of PAML output did not see seqtype' ); } my $seqtype = $self->{'_summary'}->{'seqtype'}; if ( $seqtype eq "CODONML" ) { $self->_parse_inputparams(); # settings from the .ctl file
# that get printed
$self->_parse_patterns(); # codon patterns - not very interesting
$self->_parse_seqs(); # the sequences data used for analysis
$self->_parse_codoncts(); # counts and distributions of codon/nt
# usage
$self->_parse_codon_freqs(); # codon frequencies
$self->_parse_distmat(); # NG distance matrices
} elsif ( $seqtype eq "AAML" ) { $self->_parse_inputparams; $self->_parse_patterns(); $self->_parse_seqs(); # the sequences data used for analysis
$self->_parse_aa_freqs(); # AA frequencies
# get AA distances
$self->{'_summary'}->{'aadistmat'} = $self->_parse_aa_dists(); } elsif ( $seqtype eq "CODON2AAML" ) { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'CODON2AAML parsing not yet implemented!' ); } elsif ( $seqtype eq "BASEML" ) { $self->_parse_patterns(); $self->_parse_seqs(); $self->_parse_nt_freqs(); } elsif ( $seqtype eq "YN00" ) { $self->_parse_codon_freqs(); $self->_parse_codoncts(); $self->_parse_distmat(); # NG distance matrices
} else { $self->throw( -class => 'Bio::Root::NotImplemented', -text => 'Unknown seqtype, not yet implemented!', -value => $seqtype ); }
}
_parse_inputparamsdescriptionprevnextTop
sub _parse_inputparams {
    my ($self) = @_;
    while ( defined( $_ = $self->_readline ) ) {
        if (/^((?:Codon frequencies)|(?:Site-class models))\s*:\s+(.+)/) {
            my ( $param, $val ) = ( $1, $2 );
            $self->{'_summary'}->{'inputparams'}->{$param} = $val;
        }
        elsif (/^\s+$/) {
            next;
        }
        elsif ( /^ns\s+=\s+/ || /^Frequencies/ ) {
            $self->_pushback($_);
            last;
        }
    }
}
_parse_codon_freqsdescriptionprevnextTop
sub _parse_codon_freqs {
    my ($self) = @_;
    my ( $okay, $done ) = ( 0, 0 );

    while ( defined( $_ = $self->_readline ) ) {
        if (/^Nei|\(A\) Nei/) { $self->_pushback($_); last }
        last if ($done);
        next if (/^\s+/);
        next
          unless ( $okay || /^Codon position x base \(3x4\) table\, overall/ );
        $okay = 1;
        if (s/^position\s+(\d+):\s+//) {
            my $pos = $1;
            s/\s+$//;
            my @bases = split;
            foreach my $str (@bases) {
                my ( $base, $freq ) = split( /:/, $str, 2 );
                $self->{'_summary'}->{'codonposition'}->[ $pos - 1 ]->{$base} =
                  $freq;
            }
            $done = 1 if $pos == 3;
        }
    }
    $done = 0;
    while ( defined( $_ = $self->_readline ) ) {
        if (/^Nei\s\&\sGojobori|\(A\)\sNei-Gojobori/) {
            $self->_pushback($_);
            last;
        }
        last if ($done);
        if (/^Codon frequencies under model, for use in evolver/) {
            while ( defined( $_ = $self->_readline ) ) {
                last if (/^\s+$/);
                s/^\s+//;
                s/\s+$//;
                push @{ $self->{'_summary'}->{'codonfreqs'} }, [split];
            }
            $done = 1;
        }
    }
}
_parse_aa_freqsdescriptionprevnextTop
sub _parse_aa_freqs {
    my ($self) = @_;
    my ( $okay, $done, $header ) = ( 0, 0, 0 );
    my (@bases);
    my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] };
    while ( defined( $_ = $self->_readline ) ) {
        if ( /^TREE/ || /^AA distances/ ) {
            $self->_pushback($_);
            last;
        }
        last if ($done);
        next if ( /^\s+$/ || /^\(Ambiguity/ );
        if (/^Frequencies\./) {
            $okay = 1;
        }
        elsif ( !$okay ) {    # skip till we see 'Frequencies.
next; } elsif ( !$header ) { s/^\s+//; # remove leading whitespace
@bases = split; # get an array of the all the aa names
$header = 1; $self->{'_summary'}->{'aafreqs'} = {}; # reset/clear values
next; } elsif ( /^\#\s+constant\s+sites\:\s+
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/x
) { $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; } elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) { $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; $done = 1; # done for sure
} else { my ( $seqname, @freqs ) = split; my $basect = 0; foreach my $f (@freqs) { # this will also store 'Average'
$self->{'_summary'}->{'aafreqs'}->{$seqname} ->{ $bases[ $basect++ ] } = $f; } } } } # This is for parsing the automatic tree output
}
_parse_StarDecompositiondescriptionprevnextTop
sub _parse_StarDecomposition {
    my ($self) = @_;
    my %data;

    return %data;
}
_parse_aa_distsdescriptionprevnextTop
sub _parse_aa_dists {
    my ($self) = @_;
    my ( $okay, $seen, $done ) = ( 0, 0, 0 );
    my ( %matrix, @names, @values );
    my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] };
    my $type = '';
    while ( defined( $_ = $self->_readline ) ) {
        last if $done;
        if (/^TREE/) { $self->_pushback($_); last; }
        if (/^\s+$/) {
            last if ($seen);
            next;
        }
        if (/^(AA|ML) distances/) {
            $okay = 1;
            $type = $1;
            next;
        }
        s/\s+$//g;    # remove trailing space
if ($okay) { my ( $seqname, @vl ) = split; $seen = 1; my $i = 0; # hacky workaround to problem with 3.14 aaml
if ( $type eq 'ML' && !@names && # first entry
@vl ) { # not empty
push @names, $self->{'_summary'}->{'seqs'}->[0]->display_id; } for my $s (@names) { last unless @vl; $matrix{$seqname}->{$s} = $matrix{$s}->{$seqname} = shift @vl; } push @names, $seqname; $matrix{$seqname}->{$seqname} = 0; } $done = 1 if ( scalar @names == $numseqs ); } my %dist; my $i = 0; @values = (); foreach my $lname (@names) { my @row; my $j = 0; foreach my $rname (@names) { my $v = $matrix{$lname}->{$rname}; $v = $matrix{$rname}->{$lname} unless defined $v; push @row, $v; $dist{$lname}{$rname} = [ $i, $j++ ]; } $i++; push @values,\@ row; } return new Bio::Matrix::PhylipDist( -program => $self->{'_summary'}->{'seqtype'}, -matrix =>\% dist, -names =>\@ names, -values =>\@ values );
}
_parse_patternsdescriptionprevnextTop
sub _parse_patterns {
    my ($self) = @_;
    my ( $patternct, @patterns, $ns, $ls );
    return if exists $self->{'_summary'}->{'patterns'};

    while ( defined( $_ = $self->_readline ) ) {
        if ( /^Codon\s+(usage|position)/ || /Model/ ) {
            $self->_pushback($_);
            last;
        }
        elsif ($patternct) {

            #	    last unless ( @patterns == $patternct );
last if (/^\s+$/); s/^\s+//; push @patterns, split; } elsif (/^ns\s+\=\s*(\d+)\s+ls\s+\=\s*(\d+)/) { ( $ns, $ls ) = ( $1, $2 ); } elsif (/^\# site patterns \=\s*(\d+)/) { $patternct = $1; } else { # $self->debug("Unknown line: $_");
} } $self->{'_summary'}->{'patterns'} = { -patterns =>\@ patterns, -ns => $ns, -ls => $ls };
}
_parse_seqsdescriptionprevnextTop
sub _parse_seqs {
    # this should in fact be packed into a Bio::SimpleAlign object instead of
# an array but we'll stay with this for now
my ($self) = @_; # Use this flag to deal with paml 4 vs 3 differences
# In PAML 4 the sequences precede the CODONML|BASEML|AAML
# while in PAML3 the files start off with this
return 1 if $self->{'_already_parsed_seqs'}; my ( @firstseq, @seqs ); while ( defined( $_ = $self->_readline ) ) { if (/^(Printing|After|TREE|Codon)/) { $self->_pushback($_); last; } last if ( /^\s+$/ && @seqs > 0 ); next if (/^\s+$/); next if (/^\d+\s+$/); # we are reading PHYLIP format
my ( $name, $seqstr ) = split( /\s+/, $_, 2 ); $seqstr =~ s/\s+//g; # remove whitespace
unless (@firstseq) { @firstseq = split( //, $seqstr ); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } else { my $i = 0; my $v; while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { # replace the '.' with the correct seq from the
substr( $seqstr, $v, 1, $firstseq[$v] ); $i = $v; } push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } } if ( @seqs > 0 ) { $self->{'_summary'}->{'seqs'} =\@ seqs; $self->{'_already_parsed_seqs'} = 1; } 1;
}
_parse_distmatdescriptionprevnextTop
sub _parse_distmat {
    my ($self) = @_;
    my @results;
    my $ver = 3.14;
	my $firstseq, my $secondseq;

    while ( defined( $_ = $self->_readline ) ) {
        next if /^\s+$/;

        # We need to get the names of the sequences if this is from YN00:
if (/^\(A\)\sNei-Gojobori\s\(1986\)\smethod/) { $ver = 3.15; while ( defined( $_ = $self->_readline ) ) { if ($_ =~ m/.*\d+?\.\d+?\s*\(.*/) {
$secondseq = $_;
last; } $firstseq = $_; } } last; } #return unless (/^Nei\s*\&\s*Gojobori/);
# skip the next 3 lines
if ( $self->{'_summary'}->{'seqtype'} eq 'CODONML' ) { $self->_readline; $self->_readline; $self->_readline; } my $seqct = 0; my @seqs; if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { if ($firstseq) { $firstseq =~ s/(.+?)\s+.*/$1/; $secondseq =~ s/(.+?)\s+.*/$1/; chomp $firstseq; chomp $secondseq; push @seqs, Bio::PrimarySeq->new( -display_id => $firstseq ); push @seqs, Bio::PrimarySeq->new( -display_id => $secondseq ); } } while ( defined( $_ = $self->_readline ) ) { last if ( /^\s+$/ && exists $self->{'_summary'}->{'ngmatrix'} ); next if ( /^\s+$/ || /^NOTE:/i ); chomp; $_ =~ m/(.+?)\s*(-*\d+?\.\d+?.*)/;
my $seq = $1; my $rest = $2; $rest = '' unless defined $rest; # get rid of empty messages
my $j = 0; if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { push @seqs, Bio::PrimarySeq->new( -display_id => $seq ); } while ($rest && $rest =~ /(\-?\d+(\.\d+)?)\s*\(\-?(\d+(\.\d+)?)\s+(\-?\d+(\.\d+)?)\)/g ) { $self->{'_summary'}->{'ngmatrix'}->[ $j++ ]->[$seqct] = { 'omega' => $1, 'dN' => $3, 'dS' => $5 }; } $seqct++; } if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' && @seqs ) { $self->{'_summary'}->{'seqs'} =\@ seqs; } 1;
}
_parse_PairwiseCodondescriptionprevnextTop
sub _parse_PairwiseCodon {
    my ($self) = @_;
    my @result;
    my ( $a, $b, $log, $model, $t, $kappa, $omega, $fixedkappa );
    # check to see if we have a fixed kappa:
if ( $self->{'_summary'}->{'model'} =~ /kappa = (\d+?\.\d+?) fixed/) { $fixedkappa = $1; } while ( defined( $_ = $self->_readline ) ) { if (/^pairwise comparison, codon frequencies\:\s*(\S+)\./) { $model = $1; } # 1st line of a pair block, e.g.
# 2 (all_c7259) ... 1 (all_s57600)
elsif (/^(\d+)\s+\((\S+)\)\s+\.\.\.\s+(\d+)\s+\((\S+)\)/) { ( $a, $b ) = ( $1, $3 ); } # 2nd line of a pair block, e.g.
# lnL = -126.880601
elsif (/^lnL\s+\=\s*(\-?\d+(\.\d+)?)/) { $log = $1; if ( defined( $_ = $self->_readline ) ) { # 3rd line of a pair block, e.g.
# 0.19045 2.92330 0.10941
s/^\s+//; ( $t, $kappa, $omega ) = split; # if there was a fixed kappa, there will only be two values here ($t, $omega) and $kappa = $fixedkappa.
if ($omega eq "") { $omega = $kappa; $kappa = $fixedkappa; } } } # 5th line of a pair block, e.g.
# t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353
# OR lines like (note last field; this includes a fix for bug #3040)
# t= 0.0439 S= 0.0 N= 141.0 dN/dS= 0.1626 dN= 0.0146 dS= nan
elsif (m/^t\=\s*(\d+(\.\d+)?)\s+/)
{
# Breaking out each piece individually so that you can see
# what each regexp actually looks for
my
$parse_string = $_;
$parse_string =~ m/.*t\s*\=\s*(\d+?\.\d+?)\s/;
my $temp_t = $1; $parse_string =~ m/\sS\s*\=\s*(\d+?\.\d+?)\s/;
my $temp_S = $1; $parse_string =~ m/\sN\s*\=\s*(\d+?\.\d+?)\s/;
my $temp_N = $1; $parse_string =~ m/\sdN\/dS\s*\=\s*(\d+?\.\d+?)\s/;
my $temp_omega = $1; $parse_string =~ m/\sdN\s*\=\s*(\d+?\.\d+?)\s/;
my $temp_dN = $1; $parse_string =~ m/\sdS\s*\=\s*(.+)\s/;
my $temp_dS = $1; $result[ $b - 1 ]->[ $a - 1 ] = { 'lnL' => $log, 't' => defined $t && length($t) ? $t : $temp_t, 'S' => $temp_S, 'N' => $temp_N, 'kappa' => $kappa, 'omega' => defined $omega && length($omega) ? $omega : $temp_omega, 'dN' => $temp_dN, 'dS' => $temp_dS }; } # 4th line of a pair block (which is blank)
elsif (/^\s+$/) { next; } elsif (/^\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)/) { } else { $self->debug("unknown line: $_"); } } return ( -mlmatrix =>\@ result );
}
_parse_YN_PairwisedescriptionprevnextTop
sub _parse_YN_Pairwise {
    my ($self) = @_;
    my @result;
    while ( defined( $_ = $self->_readline ) ) {
        last if (/^seq\.\s+seq\./);
    }
    while ( defined( $_ = $self->_readline ) ) {
        if (
            m/^\s+(\d+)\s+  # seq #
(\d+)\s+ # seq #
(\d+(\.\d+))\s+ # S
(\d+(\.\d+))\s+ # N
(\d+(\.\d+))\s+ # t
(\d+(\.\d+))\s+ # kappa
(\d+(\.\d+))\s+ # omega
\-??(\d+(\.\d+))\s+ # dN
\+\-\s+
\-??(\d+(\.\d+))\s+ # dN SE
\-??(\d+(\.\d+))\s+ # dS
\+\-\s+
\-??(\d+(\.\d+))\s+ # dS SE
/ox
)
{

$result[ $2 - 1 ]->[ $1 - 1 ] = {
'S' =>
$3,
'N' =>
$5,
't' =>
$7,
'kappa' =>
$9,
'omega' =>
$11,
'dN' =>
$13,
'dN_SE' =>
$15,
'dS' =>
$17,
'dS_SE' =>
$19,
};
} elsif (/^\s+$/) { next; } elsif (/^\(C\) LWL85, LPB93 & LWLm methods/) { $self->_pushback($_); last; } } return ( -mlmatrix =>\@ result );
}
_parse_ForestrydescriptionprevnextTop
sub _parse_Forestry {
    my ($self) = @_;
    my ( $instancecount, $num_param, $loglikelihood, $score, $done,
        $treelength ) = ( 0, 0, 0, 0, 0, 0 );
    my $okay = 0;
    my ( @ids, %match, @branches, @trees );
    while ( defined( $_ = $self->_readline ) ) {
        last if $done;
        if (s/^TREE\s+\#\s*\d+:\s+//) {
            ($score) = (s/MP\s+score\:\s+(\S+)\s+$//);
            @ids = /(\d+)[\,\)]/g;
        }
        elsif (/^Node\s+\&/
            || /^\s+N37/
            || /^(CODONML|AAML|YN00|BASEML)/
            || /^\*\*/
            || /^Detailed output identifying parameters/ )
        {
            $self->_pushback($_);
            $done = 1;
            last;
        }
        elsif (/^tree\s+length\s+\=\s+(\S+)/) {
            $treelength = $1;    # not going to store this for now
# as it is directly calculated from
# $tree->total_branch_length;
} elsif (/^\s*lnL\(.+np\:\s*(\d+)\)\:\s+(\S+)/) { # elsif( /^\s*lnL\(.+\)\:\s+(\S+)/ ) {
( $num_param, $loglikelihood ) = ( $1, $2 ); } elsif (/^\(/) { s/([\,:])\s+/$1/g; my $treestr = new IO::String($_); my $treeio = Bio::TreeIO->new( -fh => $treestr, -format => 'newick' ); my $tree = $treeio->next_tree; if ($tree) { $tree->score($loglikelihood); $tree->id("num_param:$num_param"); if ( $okay > 0 ) { # we don't save the trees with the number labels
if ( !%match && @ids ) { my $i = 0; for my $m (/([^():,]+):/g) { $match{ shift @ids } = [$m]; } my %grp; while ( my $br = shift @branches ) { my ( $parent, $child ) = @$br; if ( $match{$child} ) { push @{ $match{$parent} }, @{ $match{$child} }; } else { push @branches, $br; } } if ( $self->verbose > 1 ) { for my $k ( sort { $a <=> $b } keys %match ) { $self->debug( "$k -> ", join( ",", @{ $match{$k} } ), "\n" ); } } } # Associate SEs to nodes using tags
if ( defined( $self->{_SEs} ) ) { my @SEs = split( " ", $self->{_SEs} ); my $i = 0; foreach my $parent_id ( map { /\d+\.\.(\d+)/ } split( " ", $self->{_branch_ids} ) ) { my @nodes; my @node_ids = @{ $match{$parent_id} }; my @nodes_L = map { $tree->find_node( -id => $_ ) } @node_ids; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn( "no node could be found for node in SE assignation (no lca?)" ); } $n->add_tag_value( 'SE', $SEs[$i] ); $i++; } } push @trees, $tree; } } $okay++; } elsif (/^SEs for parameters/) { my $se_line = $self->_readline; $se_line =~ s/\n//; $self->{_SEs} = $se_line; } elsif (/^\s*\d+\.\.\d+/) { push @branches, map { [ split( /\.\./, $_ ) ] } split; my $ids = $_; $ids =~ s/\n//; $self->{_branch_ids} = $ids; } } return\@ trees,\% match;
}
_parse_NSsitesBatchdescriptionprevnextTop
sub _parse_NSsitesBatch {
    my $self = shift;
    my ( %data, $idlookup );
    my ( $okay, $done ) = ( 0, 0 );
    while ( defined( $_ = $self->_readline ) ) {
        last if $done;
        next if /^\s+$/;
        next unless ( $okay || /^Model\s+\d+/ || /^TREE/ );

        if (/^Model\s+(\d+)/) {
            if ($okay) {

                # this only happens if $okay was already 1 and
# we hit a Model line
$self->_pushback($_); $done = 1; } else { chomp; $data{'-model_num'} = $1; ( $data{'-model_description'} ) = (/\:\s+(.+)/); $okay = 1; } } elsif (/^Time used\:\s+(\S+)/) { $data{'-time_used'} = $1; $done = 1; } elsif (/^kappa\s+\(ts\/tv\)\s+\=\s+(\S+)/) { $data{'-kappa'} = $1; } elsif (/^TREE/) { $self->_pushback($_); ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; if ( defined $data{'-trees'} && scalar @{ $data{'-trees'} } ) { $data{'-likelihood'} = $data{'-trees'}->[0]->score; } $okay = 1; } elsif (/^omega\s+\(dn\/ds\)\s+\=\s+(\S+)/i) { # for M0 (single ratio for the entire tree)
# explicitly put '1.00000' rather than '1', because \d+\.\d{5}
# is reported in all other cases.
my @p = (q//1.00000/); # since there is only one class,
my @w = $1;
$data{'-dnds_site_classes'} = { 'p' =>\@ p, 'w' =>\@ w }; # since no K=X is provided, put 1 here
$data{q//-num_site_classes/} = 1;
} elsif ( /^(Naive Empirical Bayes)|(Bayes Empirical Bayes)|(Positively\sselected\ssites)/i ) { $self->_pushback($_); my ( $sites, $neb, $beb ) = $self->_parse_Pos_selected_sites; $data{'-pos_sites'} = $sites; $data{'-neb_sites'} = $neb; $data{'-beb_sites'} = $beb; } elsif (/^dN/i) { if (/K\=(\d+)/) { $data{'-num_site_classes'} = $1; while ( $_ = $self->_readline ) { unless ( $_ =~ /^\s+$/ ) { $self->_pushback($_); last; } } if (/^site class/) { $self->_readline; my $tmp = $self->_readline; my @p = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @b_w = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @f_w = $tmp =~ /(\d+\.\d{5})/g; my @w; foreach my $i ( 0 .. $#b_w ) { push @w, { q//background/ => $b_w[$i], q//foreground/ => $f_w[$i] }; } $data{'-dnds_site_classes'} = { q//p/ =>\@ p, q//w/ =>\@ w }; } else { my $tmp = $self->_readline; my @p = $tmp =~ /(\d+\.\d{5})/g; $tmp = $self->_readline; my @w = $tmp =~ /(\d+\.\d{5})/g; $data{'-dnds_site_classes'} = { 'p' =>\@ p, 'w' =>\@ w }; } } elsif (/for each branch/) { my %branch_dnds = $self->_parse_branch_dnds; if ( !defined $data{'-trees'} ) { $self->warn( "No trees have been loaded, can't do anything\n"); next; } my ($tree) = @{ $data{'-trees'} }; if ( !$tree || !ref($tree) || !$tree->isa('Bio::Tree::Tree') ) { $self->warn("no tree object already stored!\n"); next; } # These need to be added to the Node/branches
while ( my ( $k, $v ) = each %branch_dnds ) { # we can probably do better by caching at some point
my @nodes; for my $id ( split( /\.\./, $k ) ) { my @nodes_L = map { $tree->find_node( -id => $_ ) } @{ $idlookup->{$id} }; my $n = @nodes_L < 2 ? shift(@nodes_L) : $tree->get_lca(@nodes_L); if ( !$n ) { $self->warn( "no node could be found for $id (no lca?)"); } unless ( $n->is_Leaf && $n->id ) { $n->id($id); } push @nodes, $n; } my ( $parent, $child ) = @nodes; while ( my ( $kk, $vv ) = each %$v ) { $child->add_tag_value( $kk, $vv ); } } } } elsif (/^Parameters in beta:/) { $_ = $self->_readline; # need the next line
if (/p\=\s+(\S+)\s+q\=\s+(\S+)/) { $data{'-shape_params'} = { 'shape' => 'beta', 'p' => $1, 'q' => $2 }; } else { $self->warn("unparseable beta parameters: $_"); } } elsif (/^Parameters in beta\&w\>1:/) { # Parameters in beta&w>1:
# p0= 1.00000 p= 0.07642 q= 0.85550
# (p1= 0.00000) w= 1.00000
$_ = $self->_readline; # need the next line
my ( $p0, $p, $q, $p1, $w ); if (/p0\=\s+(\S+)\s+p\=\s+(\S+)\s+q\=\s+(\S+)/) { $p0 = $1; $p = $2; $q = $3; } else { $self->warn("unparseable beta parameters: $_"); } $_ = $self->_readline; # need the next line
if (/\(p1\=\s+(\S+)\)\s+w\=\s*(\S+)/) { $p1 = $1; $w = $2; $data{'-shape_params'} = { 'shape' => 'beta', 'p0' => $p0, 'p' => $p, 'q' => $q, 'p1' => $p1, 'w' => $w }; } else { $self->warn("unparseable beta parameters: $_"); } } elsif (/^alpha\s+\(gamma\)\s+\=\s+(\S+)/) { my $gamma = $1; $_ = $self->_readline; my ( @r, @f ); if (s/^r\s+\(\s*\d+\)\:\s+//) { @r = split; } $_ = $self->_readline; if (s/^f\s*\:\s+//) { @f = split; } $data{'-shape_params'} = { 'shape' => 'alpha', 'gamma' => $gamma, 'r' =>\@ r, 'f' =>\@ f }; } } return new Bio::Tools::Phylo::PAML::ModelResult(%data);
}
_parse_Pos_selected_sitesdescriptionprevnextTop
sub _parse_Pos_selected_sites {
    my $self    = shift;
    my $okay    = 0;
    my (%sites) = (
        'default' => [],
        'neb'     => [],
        'beb'     => []
    );
    my $type = 'default';
    while ( defined( $_ = $self->_readline ) ) {
        next if ( /^\s+$/ || /^\s+Pr\(w\>1\)/ );
        if ( /^Time used/ || /^TREE/ ) {
            $self->_pushback($_);
            last;
        }
        if (/^Naive Empirical Bayes/i) {
            $type = 'neb';
        }
        elsif (/^Bayes Empirical Bayes/i) {
            $type = 'beb';
        }
        elsif (/^Positively selected sites/) {
            $okay = 1;
        }
        elsif ( $okay
            && /^\s+(\d+)\s+(\S+)\s+(\-?\d+(?:\.\d+)?)(\**)\s+(\-?\d+(?:\.\d+)?)\s+\+\-\s+(\-?\d+(?:\.\d+)?)/
          )
        {
            my $signif = $4;
            $signif = '' unless defined $signif;
            push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5, $6 ];
        }
        elsif ( $okay
            && /^\s+(\d+)\s+(\S+)\s+(\-?\d*(?:.\d+))(\**)\s+(\-?\d+(?:\.\d+)?)/
          )
        {
            my $signif = $4;
            $signif = '' unless defined $signif;
            push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5 ];
        }
        elsif ( $okay && /^\s+(\d+)\s+(\S)\s+([\d\.\-\+]+)(\**)/ ) {
            my $signif = $4;
            $signif = '' unless defined $signif;
            push @{ $sites{$type} }, [ $1, $2, $3, $signif ];
        }
    }
    return ( $sites{'default'}, $sites{'neb'}, $sites{'beb'} );
}
_parse_branch_dndsdescriptionprevnextTop
sub _parse_branch_dnds {
    my $self = shift;
    my ($okay) = (0);
    my %branch_dnds;
    my @header;
    while ( defined( $_ = $self->_readline ) ) {
        next if (/^\s+$/);
        next unless ( $okay || /^\s+branch\s+t/ );
        if (/^\s+branch\s+(.+)/) {
            s/^\s+//;
            @header = split( /\s+/, $_ );
            $okay = 1;
        }
        elsif (/^\s*(\d+\.\.\d+)/) {
            my $branch = $1;
            s/^\s+//;
            my $i = 0;

            # fancyness just maps the header names like 't' or 'dN'
# into the hash so we get at the end of the day
# 't' => 0.067
# 'dN'=> 0.001
$branch_dnds{$branch} = { map { $header[ $i++ ] => $_ } split }; } else { $self->_pushback($_); last; } } return %branch_dnds; } #baseml stuff
}
_parse_nt_freqsdescriptionprevnextTop
sub _parse_nt_freqs {
    my ($self) = @_;
    my ( $okay, $done, $header ) = ( 0, 0, 0 );
    my (@bases);
    my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] };
    while ( defined( $_ = $self->_readline ) ) {
        if ( /^TREE/ || /^Distances/ ) { $self->_pushback($_); last }
        last if ($done);
        next if ( /^\s+$/ || /^\(Ambiguity/ );
        if (/^Frequencies\./) {
            $okay = 1;
        }
        elsif ( !$okay ) {    # skip till we see 'Frequencies.
next; } elsif ( !$header ) { s/^\s+//; # remove leading whitespace
@bases = split; # get an array of the all the aa names
$header = 1; $self->{'_summary'}->{'ntfreqs'} = {}; # reset/clear values
next; } elsif ( /^\#\s+constant\s+sites\:\s+
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/ox
) { $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; } elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) { $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; $done = 1; # done for sure
} else { my ( $seqname, @freqs ) = split; my $basect = 0; foreach my $f (@freqs) { # this will also store 'Average'
$self->{'_summary'}->{'ntfreqs'}->{$seqname} ->{ $bases[ $basect++ ] } = $f; } } }
}
_parse_nt_distsdescriptionprevnextTop
sub _parse_nt_dists {
    my ($self) = @_;
    my ( $okay, $seen, $done ) = ( 0, 0, 0 );
    my ( %matrix, @names );
    my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] };
    my $type = '';
    while ( defined( $_ = $self->_readline ) ) {
        if (/^TREE/) { $self->_pushback($_); last; }
        last if $done;
        next if (/^This matrix is not used in later/);
        if (/^\s+$/) {
            last if ($seen);
            next;
        }
        if (/^Distances:(\S+)\s+\(([^\)]+)\)\s+\(alpha set at (\-?\d+\.\d+)\)/)
        {
            $okay = 1;
            $type = $1;
            next;
        }
        s/\s+$//g;    # remove trailing space
if ($okay) { my ( $seqname, $vl ) = split( /\s+/, $_, 2 ); $seen = 1; my $i = 0; if ( defined $vl ) { while ( $vl =~ /(\-?\d+\.\d+)\s*\(\s*(\-?\d+\.\d+)\s*\)\s*/g ) { my ( $kappa, $alpha ) = ( $1, $2 ); $matrix{$seqname}{ $names[$i] } = $matrix{ $names[$i] }{$seqname} = [ $kappa, $alpha ]; $i++; } unless ($i) { $self->warn("no matches for $vl\n"); } } push @names, $seqname; $matrix{$seqname}->{$seqname} = [ 0, 0 ]; } $done = 1 if ( scalar @names == $numseqs ); } my %dist; my $i = 0; my ( @kvalues, @avalues ); foreach my $lname (@names) { my ( @arow, @krow ); my $j = 0; foreach my $rname (@names) { my $v = $matrix{$lname}{$rname}; push @krow, $v->[0]; # kappa values
push @arow, $v->[1]; # alpha
$dist{$lname}{$rname} = [ $i, $j++ ]; } $i++; push @kvalues,\@ krow; push @avalues,\@ arow; } return ( Bio::Matrix::PhylipDist->new( -program => $self->{'_summary'}->{'seqtype'}, -matrix =>\% dist, -names =>\@ names, -values =>\@ kvalues ), Bio::Matrix::PhylipDist->new( -program => $self->{'_summary'}->{'seqtype'}, -matrix =>\% dist, -names =>\@ names, -values =>\@ avalues ) ); } # BASEML
}
_parse_rate_parametesdescriptionprevnextTop
sub _parse_rate_parametes {
    my $self = shift;
    my (%rate_parameters);
    while ( defined( $_ = $self->_readline ) ) {
        if (/^Rate\s+parameters:\s+/) {
            s/\s+$//;
            $rate_parameters{'rate_parameters'} = [ split( /\s+/, $_ ) ];
        }
        elsif (/^Base\s+frequencies:\s+/) {
            s/\s+$//;
            $rate_parameters{'base_frequencies'} = [ split( /\s+/, $_ ) ];
        }
        elsif (
            m/^Rate\s+matrix\s+Q,\s+Average\s+Ts\/Tv\s+(\([^\)+]+\))?\s*\=\s+
(\-?\d+\.\d+)/x
)
{
$rate_parameters{'average_TsTv'} = $1;
while ( defined( $_ = $self->_readline ) ) { # short circuit
last if (/^\s+$/); if (/^alpha/) { $self->_pushback($_); last; } s/^\s+//; s/\s+$//; push @{ $rate_parameters{'rate_matrix_Q'} }, [split]; } } elsif (/^alpha\s+\(gamma,\s+K=\s*(\d+)\s*\)\s*\=\s*(\-?\d+\.\d+)/) { $rate_parameters{'K'} = $1; $rate_parameters{'alpha'} = $2; } elsif (s/^(r|f):\s+//) { my ($p) = $1; s/\s+$//; $rate_parameters{$p} = [split]; } } } # RST parsing
}
_parse_rstdescriptionprevnextTop
sub _parse_rst {
    my ($self) = @_;
    return unless $self->{'_dir'} && -d $self->{'_dir'} && -r $self->{'_dir'};

    my $rstfile = File::Spec->catfile( $self->{'_dir'}, $RSTFILENAME );
    return unless -e $rstfile && !-z $rstfile;
    my $rstio = Bio::Root::IO->new( -file => $rstfile );

    # define whatever data structures you need to store the data
# key points are to reuse existing bioperl objs (like Bio::Seq)
# where appropriate
my ( @firstseq, @seqs, @trees, @per_site_prob ); my $count; while ( defined( $_ = $rstio->_readline ) ) { # implement the parsing here
if (/^TREE\s+\#\s+(\d+)/) { while ( defined( $_ = $rstio->_readline ) ) { if (/tree\s+with\s+node\s+labels\s+for/) { my $tree = Bio::TreeIO->new( -noclose => 1, -fh => $rstio->_fh, -format => 'newick' )->next_tree; # cleanup leading/trailing whitespace
for my $n ( $tree->get_nodes ) { my $id = $n->id; $id =~ s/^\s+//; $id =~ s/\s+$//; $n->id($id); if ( defined( my $blen = $n->branch_length ) ) { $blen =~ s/^\s+//; $blen =~ s/\s+$//; $n->branch_length($blen); } } push @trees, $tree; last; } } } elsif (/^Prob\sof\sbest\scharacter\sat\seach\snode,\slisted\sby\ssite/) { $self->{'_rst'}->{'persite'} = []; while ( defined( $_ = $rstio->_readline ) ) { next if ( /^Site/i || /^\s+$/ ); if (s/^\s+(\d+)\s+(\d+)\s+([^:]+)\s*:\s*(.+)//) { my ( $sitenum, $freq, $extant, $ancestral ) = ( $1, $2, $3, $4 ); my ( @anc_site, @extant_site ); @extant_site = {}; while ( $extant =~ s/^([A-Z\-]{3})\s+\(([A-Z*])\)\s+//g ) { push @extant_site, { 'codon' => $1, 'aa' => $2 }; } while ( $ancestral =~ s/^([A-Z\-]{3})\s+([A-Z*])\s+ # codon AA
(\S+)\s+ # Prob
\(([A-Z*])\s+(\S+)\)\s*//xg
# AA Prob
) { push @anc_site, { 'codon' => $1, 'aa' => $2, 'prob' => $3, 'Yang95_aa' => $4, 'Yang95_aa_prob' => $5 }; } # saving persite
$self->{'_rst'}->{'persite'}->[$sitenum] = [ @extant_site, @anc_site ]; } elsif (/^Summary\sof\schanges\salong\sbranches\./) { last; } } } elsif (/^Check\sroot\sfor\sdirections\sof\schange\./ || /^Summary\sof\schanges\salong\sbranches\./ ) { my ( @branches, @branch2node, $branch, $node ); my $tree = $trees[-1]; if ( !$tree ) { $self->warn("No tree built before parsing Branch changes\n"); last; } my @nodes = ( map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [ $_, $_->id =~ /^(\d+)\_?/ ] } $tree->get_nodes ); unshift @nodes, undef; # fake first node so that index will match nodeid
while ( defined( $_ = $rstio->_readline ) ) { next if /^\s+$/; if (m/^List\sof\sextant\sand\sreconstructed\ssequences/) {
$rstio->_pushback($_);
last; } elsif (/^Branch\s+(\d+):\s+(\d+)\.\.(\d+)\s+/) { my ( $left, $right ); ( $branch, $left, $right ) = ( $1, $2, $3 ); ($node) = $nodes[$right]; if ( !$node ) { $self->warn( "cannot find $right in $tree ($branch $left..$right)\n" ); last; } if (/\(n=\s*(\S+)\s+s=\s*(\S+)\)/) { $node->add_tag_value( 'n', $1 ); $node->add_tag_value( 's', $2 ); } $branch2node[$branch] = $right; } elsif ( /^\s+(\d+)\s+([A-Z*])\s+(\S+)\s+\-\>\s+([A-Z*])\s+(\S+)?/) { my ( $site, $anc, $aprob, $derived, $dprob ) = ( $1, $2, $3, $4, $5 ); if ( !$node ) { $self->warn("no branch line was previously parsed!"); next; } my %c = ( 'site' => $site, 'anc_aa' => $anc, 'anc_prob' => $aprob, 'derived_aa' => $derived, ); $c{'derived_prob'} = $dprob if defined $dprob; $node->add_tag_value( 'changes',\% c ); } } } elsif ( /^Overall\s+accuracy\s+of\s+the\s+(\d+)\s+ancestral\s+sequences:/) { my $line = $rstio->_readline; $line =~ s/^\s+//; $line =~ s/\s+$//; my @overall_site = split( /\s+/, $line ); # skip next 2 lines, want the third
for ( 1 .. 3 ) { $line = $rstio->_readline; } $line =~ s/^\s+//; $line =~ s/\s+$//; my @overall_seq = split( /\s+/, $line ); if ( @overall_seq != @overall_site || @overall_seq != @seqs ) { $self->warn( "out of sync somehow seqs, site scores don't match\n"); $self->warn("@seqs @overall_seq @overall_site\n"); } for (@seqs) { $_->description( sprintf( "overall_accuracy_site=%s overall_accuracy_seq=%s", shift @overall_site, shift @overall_seq ) ); } } elsif (m/^List of extant and reconstructed sequences/o) {
my
$seqcount = 0;
while ( defined( $_ = $rstio->_readline ) ) { last if (/^Overall accuracy of the/); if (/^\s+$/) { last if $seqcount && $seqcount == @seqs; next; } if (/^\s*(\d+)\s+(\d+)\s+$/) { $seqcount = $1; next } # runmode = (0)
# this should in fact be packed into a Bio::SimpleAlign object
# instead of an array but we'll stay with this for now
if (/^node/) { my ( $name, $num, $seqstr ) = split( /\s+/, $_, 3 ); $name .= $num; $seqstr =~ s/\s+//g; # remove whitespace
unless (@firstseq) { @firstseq = split( //, $seqstr ); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } else { my $i = 0; my $v; while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { # replace the '.' with the correct seq from the
substr( $seqstr, $v, 1, $firstseq[$v] ); $i = $v; } $self->debug("adding seq $seqstr\n"); push @seqs, Bio::LocatableSeq->new( -display_id => $name, -seq => $seqstr ); } } } $self->{'_rst'}->{'rctrted_seqs'} =\@ seqs; } else { } } $self->{'_rst'}->{'trees'} =\@ trees; return; } 1;
}
General documentation
TO DOTop
Implement get_posteriors(). For NSsites models, obtain arrayrefs of
posterior probabilities for membership in each class for every
position; probabilities correspond to classes w0, w1, ... etc.
  my @probs = $result->get_posteriors();
# find, say, positively selected sites! if ($params->{w2} > 1) { for (my $i = 0; $i < @probs ; $i++) { if ($probs[$i]->[2] > 0.5) { # assumes model M1: three w's, w0, w1 and w2 (positive selection) printf "position %d: (%g prob, %g omega, %g mean w)\n", $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3]; } } } else { print "No positive selection found!\n"; }
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich, Aaron MackeyTop
Email jason-at-bioperl.org
Email amackey-at-virginia.edu
CONTRIBUTORSTop
Albert Vilella avilella-AT-gmail-DOT-com
Sendu Bala bix@sendu.me.uk
Dave Messina dmessina@cpan.org
TODOTop
RST parsing -- done, Avilella contributions bug#1506, added by jason 1.29
-- still need to parse in joint probability and non-syn changes
at site table
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Implement Bio::AnalysisParserI interfaceTop