Bio::Tools::Run::Phylo::PAML Yn00
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::Root
Bio::Tools::Phylo::PAML
Bio::Tools::Run::WrapperBase
Bio::TreeIO
Cwd
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'phylip',
-file => 't/data/gf-s85.phylip');
my $aln = $alignio->next_aln;
my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new(); $yn->alignment($aln); my ($rc,$parser) = $yn->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 my $dN = $MLmatrix->[0]->[1]->{dN}; my $dS = $MLmatrix->[0]->[1]->{dS}; my $kaks =$MLmatrix->[0]->[1]->{omega}; print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n"; }
Description
This is a wrapper around the yn00 (method of Yang and Nielsen, 2000)
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 yn00.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.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
runDescriptionCode
error_stringDescriptionCode
alignmentDescriptionCode
get_parametersDescriptionCode
set_parameterDescriptionCode
set_default_parametersDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $yn00->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $yn00->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::Yn00->new();
Function: Builds a new Bio::Tools::Run::Phylo::PAML::Yn00 object
Returns : Bio::Tools::Run::Phylo::PAML::Yn00
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
runcodeprevnextTop
 Title   : run
Usage : $yn->run();
Function: run the yn00 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 : none
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 : $codeml->align($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 : $codeml->set_parameter($param,$val);
Function: Sets a codeml 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:
$codeml->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 : $codeml->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
Methods code
BEGINTop
BEGIN {
 
    $MINNAMELEN = 25;
    $PROGRAMNAME = 'yn00'  . ($^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 codeml.ctl
# example file provided with the package
%VALIDVALUES = ( 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much
'weighting' => [0,1], # weighting pathways between codons
'commonf3x4' => [0,1], # use same f3x4 for all sites
# (icode) genetic code
# 0:universal code
# 1:mamalian mt
# 2:yeast mt
# 3:mold mt,
# 4:invertebrate mt
# 5:ciliate nuclear
# 6:echinoderm mt
# 7:euplotid mt
# 8:alternative yeast nu.
# 9:ascidian mt
#10:blepharisma nu
# these correspond to 1-11 in the genbank transl table
'icode' => [ 0..10], 'ndata' => [1..10], );
}
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,$st) = $self->_rearrange([qw(ALIGNMENT SAVE_TEMPFILES)],
				    @args);
  defined $aln && $self->alignment($aln);
  defined $st  && $self->save_tempfiles($st);
  
  $self->set_default_parameters();
  return $self;
}
rundescriptionprevnextTop
sub run {
   my ($self,$aln) = @_;
   ($aln) ||= $self->alignment();
   if( ! $aln ) { 
       $self->warn("must have supplied a valid alignment file in order to run yn00");
       return 0;
   }
   my ($tmpdir) = $self->tempdir();
   my ($tempseqFH,$tempseqfile);
   if( ! ref($aln) && -e $aln ) { 
       $tempseqfile = $aln;
   } else { 
       ($tempseqFH,$tempseqfile) = $self->io->tempfile
	   ('-dir' => $tmpdir, 
	    UNLINK => ($self->save_tempfiles ? 0 : 1));
       my $alnout = Bio::AlignIO->new('-format'      => 'phylip',
				     '-fh'          => $tempseqFH,
				     '-interleaved' => 0,
				     '-idlength'    => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1);
       
       $alnout->write_aln($aln);
       $alnout->close();
       undef $alnout;   
       close($tempseqFH);
       undef $tempseqFH;
   } 
   # now let's print the yn.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 $yn_ctl = "$tmpdir/yn00.ctl"; open(YN, ">$yn_ctl") or $self->throw("cannot open $yn_ctl for writing"); print YN "seqfile = $tempseqfile\n"; my $outfile = $self->outfile_name; print YN "outfile = $outfile\n"; my %params = $self->get_parameters; while( my ($param,$val) = each %params ) { print YN "$param = $val\n"; } close(YN); my ($rc,$parser) = (1); { my $cwd = cwd(); my $exit_status; chdir($tmpdir); my $ynexe = $self->executable(); $self->throw("unable to find executable for 'yn'") unless $ynexe; open(RUN, "$ynexe |"); my @output = <RUN>; $exit_status = close(RUN); $self->error_string(join('',@output)); if( (grep { /\berr(or)?: /io } @output) || !$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/mlc", -dir => "$tmpdir"); }; if( $@ ) { $self->warn($self->error_string); } chdir($cwd); } if( $self->verbose > 0 ) { open(IN, "$tmpdir/mlc"); while(<IN>) { $self->debug($_); } } unless ( $self->save_tempfiles ) { unlink("$yn_ctl"); $self->cleanup(); } return ($rc,$parser);
}
error_stringdescriptionprevnextTop
sub error_string {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};
}
alignmentdescriptionprevnextTop
sub alignment {
   my ($self,$aln) = @_;
   if( defined $aln ) { 
       if( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { 
	   $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function");
	   return undef;
       }
       $self->{'_alignment'} = $aln;
   }
   return  $self->{'_alignment'};
}
get_parametersdescriptionprevnextTop
sub get_parameters {
   my ($self) = @_;
   # we're returning a copy of this
return %{ $self->{'_codemlparams'} };
}
set_parameterdescriptionprevnextTop
sub set_parameter {
   my ($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 ) {
       
       unless ( grep {$value} @{ $VALIDVALUES{$param} } ) {
	   $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;
       }
   }
   $self->{'_codemlparams'}->{$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 $self->{'_codemlparams'}->{$param} && $keepold); if(ref($val)=~/ARRAY/i ) { $self->{'_codemlparams'}->{$param} = $val->[0]; } else { $self->{'_codemlparams'}->{$param} = $val; } }
}
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:
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Default ValuesTop
See the Bio::Tools::Run::Phylo::PAML::Codeml module for
documentation of the default values.
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)
outfile_nameTop
 Title   : outfile_name
Usage : my $outfile = $codeml->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
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 : $codeml->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