Bio::Tools::Run::Phylo::PAML Baseml
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Summary
Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Tools::Phylo::PAML
Bio::TreeIO
Cwd
Inherit
Bio::Tools::Run::Phylo::PhyloBase
Synopsis
  use Bio::Tools::Run::Phylo::PAML::Baseml;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'phylip',
-file => 't/data/gf-s85.phylip');
my $aln = $alignio->next_aln;
my $bml = Bio::Tools::Run::Phylo::PAML::Baseml->new(); $bml->alignment($aln); my ($rc,$parser) = $bml->run(); while( my $result = $parser->next_result ) { my @otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); # 0 and 1 correspond to the 1st and 2nd entry in the @otus array }
Description
This is a wrapper around the baseml program of PAML (Phylogenetic
Analysis by Maximum Likelihood) package of Ziheng Yang. See
http://abacus.gene.ucl.ac.uk/software/paml.html for more information.
This module will generate a proper baseml.ctl file and will run the
program in a separate temporary directory to avoid creating temp files
all over the place and will cleanup after itself..
The values you can feed to the configuration file are documented here.
    'noisy'   => [ 0..3,9],
'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much
'runmode' => [0..5],
# for runmode
# 0: use the provided tree structure(s) in treefile
# 1,2: mean heuristic search by star-decomposition alg
# 2: starts from star tree while 1 reads a multifurcating
# tree from treefile and ties to estimate the best
# bifurcating tree
# 3: stepwise addition
# 4: NNI perturbation with the starting tree
# Tree search DOES NOT WORK WELL so estimate a tree
# using other programs first
'model' => '0',
# for model
# 0: JC69 (uncorrected)
# 1: K80 (transitions/transversion weighted differently)
# 2: F81
# 3: F84
# 4: HKY85
# 5: T92 (Tamura 92)
# 6: TN93 (Tajima-Nei) correct for multiple substitutions
# 7: REV (aka GTR)
# 8: UNREST
# 9: REVu
#10: UNRESTu
# See Yang 1994 JME 39:105-111
# model 8 special case of the REV model # model 9 is special case of unrestricted model # can also supply special rate parameters # so for example (from pamlDOC.pdf # $model = '8 [2 (CT) (AG)]'; # TN93 # $model = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93 # $model = '9 [1 (TC CT AG GA)]; # K80 # $model = '9 [0]'; # JC69 # $model = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)], 'outfile' => 'mlb', 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa 'kappa' => '2.5', # initial or fixed kappa 'fix_alpha'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'alpha' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'Malpha' => [0,1], # different alphas for genes 'fix_rho'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'rho' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'ncatG' => '5', # number of categories in the dD,AdG, or nparkK models of rates 'nparK' => [0..4], # rate-class models # 1:rk 2:rk&fK # 3:rK&MK(1/K) 4:rK&MK 'nhomo' => [0..4], # 0 & 1: homogeneous, # 2: kappa for brances # 3:N1 4:N2 'getSE' => [0,1], 'RateAncestor' => [1,0,2], # rates (alpha > 0) or # ancestral states 'cleandata' => [1,0], # remove sites with # ambiguity data (1:yes or 0:no) 'fix_blength' => [-1,0,1,2], # 0: ignore, -1: random, # 1: initial, 2: fixed # 'icode' => [ 0..10], # (with RateAncestor=1. #try "GC" in data,model=4,Mgene=4) 'ndata' => [5,1..10], 'clock' => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis 'Small_Diff' => '1e-6', #underflow issues?
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
runDescriptionCode
error_stringDescriptionCode
alignmentDescriptionCode
tree
No description
Code
get_parametersDescriptionCode
set_parameterDescriptionCode
set_default_parametersDescriptionCode
outfile_nameDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $obj->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
newcodeprevnextTop
 Title   : new
Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Baseml->new();
Function: Builds a new Bio::Tools::Run::Phylo::PAML::Baseml object
Returns : Bio::Tools::Run::Phylo::PAML::Baseml
Args : -alignment => the Bio::Align::AlignI object
-tree => the Bio::Tree::TreeI object if you want to use runmode
0 or 1
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
runcodeprevnextTop
 Title   : run
Usage : $yn->run();
Function: run the Baseml analysis using the default or updated parameters
the alignment parameter must have been set
Returns : 3 values,
$rc = 1 for success, 0 for errors
hash reference of the Yang calculated Ka/Ks values
this is a set of pairwise observations keyed as
sequencenameA->sequencenameB->datatype
hash reference same as the previous one except it for the
Nei and Gojobori calculated Ka,Ks,omega values
Args : optionally, a value appropriate for alignment() and one for tree()
NB : Since Baseml doesn't handle spaces in tree node ids, if a tree is
in use spaces will be converted to underscores in both the tree node
ids and alignment sequence ids.
error_stringcodeprevnextTop
 Title   : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
alignmentcodeprevnextTop
 Title   : alignment
Usage : $baseml->alignment($aln);
Function: Get/Set the Bio::Align::AlignI object
Returns : Bio::Align::AlignI object
Args : [optional] Bio::Align::AlignI
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: Bio::SimpleAlign
get_parameterscodeprevnextTop
 Title   : get_parameters
Usage : my %params = $self->get_parameters();
Function: returns the list of parameters as a hash
Returns : associative array keyed on parameter names
Args : none
set_parametercodeprevnextTop
 Title   : set_parameter
Usage : $baseml->set_parameter($param,$val);
Function: Sets a baseml parameter, will be validated against
the valid values as set in the %VALIDVALUES class variable.
The checks can be ignored if on turns of param checks like this:
$baseml->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
then no warning will be reported
Args : $paramname => name of the parameter
$value => value to set the parameter to
See also: no_param_checks()
set_default_parameterscodeprevnextTop
 Title   : set_default_parameters
Usage : $baseml->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
NB : using this isn't an especially good idea! You don't need to do
anything to end up using default paramters: hence 'default'!
outfile_namecodeprevnextTop
 Title   : outfile_name
Usage : my $outfile = $baseml->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
Methods code
BEGINTop
BEGIN {
     $MINNAMELEN = 25;
    $PROGRAMNAME = 'baseml'  . ($^O =~ /mswin/i ?'.exe':'');
    if( defined $ENV{'PAMLDIR'} ) {
	$PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME);
    }
    # valid values for parameters, the default one is always
# the first one in the array
# much of the documentation here is lifted directly from the baseml.ctl
# example file provided with the package
%VALIDVALUES = ( 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much
'runmode' => [0..5], # for runmode
# 0: use the provided tree structure(s) in treefile
# 1,2: mean heuristic search by star-decomposition alg
# 2: starts from star tree while 1 reads a multifurcating
# tree from treefile and ties to estimate the best
# bifurcating tree
# 3: stepwise addition
# 4: NNI perturbation with the starting tree
# Tree search DOES NOT WORK WELL so estimate a tree
# using other programs first
'model' => [5, 0..8], # for model
# 0: JC69 (uncorrected)
# 1: K80 (transitions/transversion weighted differently)
# 2: F81
# 3: F84
# 4: HKY85
# 5: T92 (Tamura 92)
# 6: TN93 (Tajima-Nei) correct for multiple substitutions
# 7: REV (aka GTR)
# 8: UNREST
# See Yang 1994 JME 39:105-111
# model 8 special case of the REV model
# model 9 is special case of unrestricted model
# can also supply special rate parameters
# so for example (from pamlDOC.pdf
# $model = '8 [2 (CT) (AG)]'; # TN93
# $model = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93
# $model = '9 [1 (TC CT AG GA)]; # K80
# $model = '9 [0]'; # JC69
# $model = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)],
'outfile' => 'mlb', 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa
'kappa' => '2.5', # initial or fixed kappa
'fix_alpha'=> [1,0], # 0: estimate gamma shape param
# 1: fix it at alpha
'alpha' => '0', # initial of fixed alpha
# 0: infinity (constant rate)
'Malpha' => [0,1], # different alphas for genes
'fix_rho'=> [1,0], # 0: estimate gamma shape param
# 1: fix it at alpha
'rho' => '0', # initial of fixed alpha
# 0: infinity (constant rate)
'ncatG' => '5', # number of categories in the dD,AdG, or nparkK models of rates
'nparK' => [0..4], # rate-class models
# 1:rk 2:rk&fK
# 3:rK&MK(1/K) 4:rK&MK
'nhomo' => [0..4], # 0 & 1: homogeneous,
# 2: kappa for brances
# 3:N1 4:N2
'getSE' => [0,1], 'RateAncestor' => [0,1,2], # rates (alpha > 0) or
# ancestral states
'cleandata' => [1,0], # remove sites with
# ambiguity data (1:yes or 0:no)
'fix_blength' => [0,-1,1,2], # 0: ignore, -1: random,
# 1: initial, 2: fixed
'icode' => [ 0..10], # (with RateAncestor=1.
#try "GC" in data,model=4,Mgene=4)
'ndata' => [1..10], 'clock' => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis
'Small_Diff' => '1e-6', #underflow issues?
'Mgene' => [0..4], # 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
);
}
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAMNAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
            return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR};
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($aln,$tree,$st) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES)],
				    @args);
  defined $aln && $self->alignment($aln);
  defined $tree && $self->tree($tree);
  defined $st  && $self->save_tempfiles($st);
  
  return $self;
}
rundescriptionprevnextTop
sub run {
   my ($self, $aln, $tree) = @_;
   $aln = $self->alignment($aln) if $aln;
   $tree = $self->tree($tree) if $tree;
   $aln ||= $self->alignment();
   $tree ||= $self->tree();
   
   my %params = $self->get_parameters;
   if( ! $aln ) { 
       $self->warn("must have supplied a valid aligment file in order to run baseml");
       return 0;
   }
   if ((defined $params{runmode} && ($params{runmode} == 0 || $params{runmode} == 1)) && ! $tree) {
        $self->warn("must have supplied a tree in order to run baseml in runmode 0 or 1");
        return 0;
   }
   
    # replace spaces with underscores in ids, since baseml really doesn't like
# spaces (actually, the resulting double quotes) in tree ids
if ($tree) { my $changed = 0; foreach my $thing ($aln->each_seq, $tree ? $tree->get_leaf_nodes : ()) { my $id = $thing->id; if ($id =~ / /) { $id =~ s/\s+/_/g; $thing->id($id); $changed = 1; } } if ($changed) { my $new_aln = $aln->new; foreach my $seq ($aln->each_seq) { $new_aln->add_seq($seq); } $aln = $new_aln; $aln = $self->alignment($aln); $tree = $self->tree($tree); } # check node and seq names match
$self->_check_names; } # output the alignment and tree to tempfiles
my $tempseqfile = $self->_write_alignment('phylip', -interleaved => 0, -idlinebreak => 1, -line_length => 60, -wrap_sequential => 1, -idlength => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1); $tree = $self->_write_tree() if $tree; # now let's print the baseml.ctl file.
# many of the these programs are finicky about what the filename is
# and won't even run without the properly named file. Ack
my $tmpdir = $self->tempdir(); my $baseml_ctl = "$tmpdir/baseml.ctl"; open(my $mlfh, ">$baseml_ctl") or $self->throw("cannot open $baseml_ctl for writing"); print $mlfh "seqfile = $tempseqfile\n"; print $mlfh "treefile = $tree\n" if $tree; my $outfile = $self->outfile_name; print $mlfh "outfile = $outfile\n"; while( my ($param,$val) = each %params ) { next if $param eq 'outfile'; print $mlfh "$param = $val\n"; } close($mlfh); my ($rc,$parser) = (1); { my $cwd = cwd(); my $exit_status; chdir($tmpdir); my $ynexe = $self->executable(); $self->throw("unable to find executable for 'baseml'") unless $ynexe; open(my $run, "$ynexe |"); my @output = <$run>; $exit_status = close($run); $self->error_string(join('', grep { /\berr(or)?: /io } @output)); if ($self->error_string || !$exit_status) { $self->warn("There was an error - see error_string for the program output"); $rc = 0; } eval { $parser = Bio::Tools::Phylo::PAML->new(-file => "$tmpdir/mlb", -dir => "$tmpdir"); }; if( $@ ) { $self->warn($self->error_string); } chdir($cwd); } if( $self->verbose > 0 ) { open(my $in, "$tmpdir/mlb"); while(<$in>) { $self->debug($_); } close($in); } return ($rc,$parser);
}
error_stringdescriptionprevnextTop
sub error_string {
   my ($self,$value) = @_;
   if( defined $value) {
     chomp($value);
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};
}
alignmentdescriptionprevnextTop
sub alignment {
   my $self = shift;
   return $self->_alignment(@_);
}
treedescriptionprevnextTop
sub tree {
    my $self = shift;
    return $self->_tree(@_);
}
get_parametersdescriptionprevnextTop
sub get_parameters {
   my ($self) = @_;
   # we're returning a copy of this
return %{ $self->{'_basemlparams'} };
}
set_parameterdescriptionprevnextTop
sub set_parameter {
   my ($self,$param,$value) = @_;
   
   if( ! defined $VALIDVALUES{$param} ) { 
       $self->warn("unknown parameter $param will not set unless you force by setting no_param_checks to true");
       return 0;
   } 
   if( ref( $VALIDVALUES{$param}) =~ /ARRAY/i &&
       scalar @{$VALIDVALUES{$param}} > 0 ) {
       
       my %allowed = map { $_ => 1 } @{ $VALIDVALUES{$param} };
       unless ( exists $allowed{$value} ) {
	   $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value");
	   return 0;
       }
   }
   $self->{'_basemlparams'}->{$param} = $value;
   return 1;
}
set_default_parametersdescriptionprevnextTop
sub set_default_parameters {
   my ($self,$keepold) = @_;
   $keepold = 0 unless defined $keepold;
   
   while( my ($param,$val) = each %VALIDVALUES ) {
       # skip if we want to keep old values and it is already set
next if( defined $self->{'_basemlparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_basemlparams'}->{$param} = $val->[0]; } else { $self->{'_basemlparams'}->{$param} = $val; } }
}
outfile_namedescriptionprevnextTop
sub outfile_name {
    my $self = shift;
    if( @_ ) {
	return $self->{'_basemlparams'}->{'outfile'} = shift @_;
    }
    unless (defined $self->{'_basemlparams'}->{'outfile'}) {
        $self->{'_basemlparams'}->{'outfile'} = 'mlb';
    }
    return $self->{'_basemlparams'}->{'outfile'};
}
General documentation
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
Support Top
 
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:
  http://bugzilla.open-bio.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Sendu Bala - bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Tools::Run::Wrapper methodsTop
no_param_checksTop
 Title   : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
save_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
tempdirTop
 Title   : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanupTop
 Title   : cleanup
Usage : $baseml->cleanup();
Function: Will cleanup the tempdir directory after a PAML run
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none