Bio::Tools::Run::Phylo::SLR.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program

SYNOPSIS

   use Bio::Tools::Run::Phylo::SLR;
   use Bio::AlignIO;
   use Bio::TreeIO;
   use Bio::SimpleAlign;
 
   my $alignio = Bio::AlignIO->new
       (-format => 'fasta',
        -file   => 't/data/219877.cdna.fasta');
 
   my $aln = $alignio->next_aln;
 
   my $treeio = Bio::TreeIO->new
       (-format => 'newick', -file => 't/data/219877.tree');
 
   my $tree = $treeio->next_tree;
 
   my $slr = Bio::Tools::Run::Phylo::SLR->new();
   $slr->alignment($aln);
   $slr->tree($tree);
   # $rc = 1 for success, 0 for errors
   my ($rc,$results) = $slr->run();
 
   my $positive_sites = $results->{'positive'};
 
   print "# Site\tNeutral\tOptimal\tOmega\t",
         "lower\tupper\tLRT_Stat\tPval\tAdj.Pval\tResult\tNote\n";
   foreach my $positive_site (@$positive_sites) {
       print 
           $positive_site->[0], "\t",
           $positive_site->[1], "\t",
           $positive_site->[2], "\t",
           $positive_site->[3], "\t",
           $positive_site->[4], "\t",
           $positive_site->[5], "\t",
           $positive_site->[6], "\t",
           $positive_site->[7], "\t",
           $positive_site->[8], "\t",
           "positive\n";
   }
 
 

DESCRIPTION

This is a wrapper around the SLR program. See http://www.ebi.ac.uk/goldman/SLR/ for more information.

This module is more about generating the proper ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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 Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Albert Vilella

Email avilella-at-gmail-dot-com

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Default Values

INCOMPLETE DOCUMENTATION OF ALL METHODS

seqfile [incodon]
  File from which to read alignment of codon sequences. The file
  should be in PAML format.

treefile [intree]
  File from which tree should be read. The tree should be in Nexus
  format

outfile [slr.res]
  File to which results are written. If the file already exists, it will
  be overwritten.

reoptimise [1]
  Should the branch lengths, omega and kappa be reoptimized?
  0 - no
  1 - yes.

kappa [2.0]
  Value for kappa. If 'reoptimise' is specified, the value
  given will be used as am initial estimate,

omega [0.1]
  Value for omega (dN/dS). If 'reoptimise' is specified, the value
  given will be used as an initial estimate.

codonf [0]
  How codon frequencies are estimated:
    0: F61/F60  Estimates used are the empirical frequencies from the
  data.
    1: F3x4     The frequencies of nucleotides at each codon position
  are estimated from the data and then multiplied together to get the
  frequency of observing a given codon. The frequency of stop codons is
  set to zero, and all other frequencies scaled appropriately.
    2: F1x4     Nucleotide frequencies are estimated from the data
  (not taking into account at which position in the codon it occurs).
  The nucleotide frequencies are multiplied together to get the frequency 
  of observing and then corrected for stop codons.

freqtype [0]
  How codon frequencies are incorporated into the substitution matrix.
  0: q_{ij} = pi_{j} s_{ij}
  1: q_{ij} = \sqrt(pi_j/pi_i) s_{ij}
  2: q_{ij} = \pi_{n} s_{ij}, where n is the nucleotide that the 
  subsitution is to.
  3: q_{ij} = s_{ij} / pi_i
  Option 0 is the tradition method of incorporating equilibrium frequencies
  into subsitution matrices (Felsenstein 1981; Goldman and Yang, 1994)
  Option 1 is described by Goldman and Whelan (2002), in this case with the
  additional parameter set to 0.5.
  Option 2 was suggested by Muse and Gaut (1994).
  Option 3 is included as an experiment, originally suggested by Bret Larget.
  it does not appear to describe evolution very successfully and should not
  be used for analyses.

   Kosakovsky-Pond has repeatedly stated that he finds incorporating codon
   frequencies in the manner of option 2 to be superior to option 0. We find
   that option 1 tends to perform better than either of these options.
 
 

positive_only [0]
  If only positively selected sites are of interest, set this to ``1''.
  Calculation will be slightly faster, but information about sites under
  purifying selection is lost.

gencode [universal]
  Which genetic code to use when determining whether a given mutation
  is synonymous or nonsynonymous. Currently only ``universal'' and
  ``mammalian'' mitochondrial are supported.

nucleof [0]
  Allow for empirical exchangabilities for nucleotide substitution.
  0: No adjustment. All nucleotides treated the same, modulo 
  transition / transversion.
  1: The rate at which a substitution caused a mutation from nucleotide
  a to nucleotide b is adjust by a constant N_{ab}. This adjustment is 
  in addition to other adjustments (e.g. transition / transversion or
  base frequencies).

aminof [0]
  Incorporate amino acid similarity parameters into substitution matrix,
  adjusting omega for a change between amino acid i and amino acid j.
  A_{ij} is a symmetric matrix of constants representing amino acid
  similarities.
  0: Constant omega for all amino acid changes
  1: omega_{ij} = omega^{A_{ij}}
  2: omega_{ij} = a_{ij} log(omega) / [ 1 - exp(-a_{ij} log(omega)) ]
  Option 1 has the same form as the original codon subsitution model 
  proposed by Goldman and Yang (but with potentially different 
  constants).
  Option 2 has a more population genetic derivtion, with omega being
  interpreted as the ratio of fixation probabilities.

nucfile [nuc.dat]
  If nucleof is non-zero, read nucleotide substitution constants from
  nucfile. If this file does not exist, hard coded constants are used.

aminofile [amino.dat]
  If aminof is non-zero, read amino acid similarity constants from
  aminofile. If this file does not exist, hard coded constants are used.

timemem [0]
  Print summary of real time and CPU time used. Will eventually print
  summary of memory use as well.

ldiff [3.841459]
  Twice log-likelihood difference used as a threshold for calculating 
  support (confidence) intervals for sitewise omega estimates. This 
  value should be the quantile from a chi-square distribution with one
  degree of freedom corresponding to the support required. 
  E.g. qchisq(0.95,1) = 3.841459
     0.4549364 = 50% support
     1.323304  = 75% support
     2.705543  = 90% support
     3.841459  = 95% support
     6.634897  = 99% support
     7.879439  = 99.5% support
    10.82757   = 99.9% support

paramin []
  If not blank, read in parameters from file given by the argument.

paramout []
  If not blank, write out parameter estimates to file given.

skipsitewise [0]
  Skip sitewise estimation of omega. Depending on other options given, 
  either calculate maximum likelihood or likelihood fixed at parameter
  values given.

seed [0]
  Seed for random number generator. If seed is 0, then previously 
  produced seed file (~/.rng64) is used. If this does not exist, the
  random number generator is initialised using the clock.

saveseed [1]
  If non-zero, save finial seed in file (~/.rng64) to be used as initial
  seed in future runs of program.

Results Format

Results file (default: slr.res) ------------ Results are presented in nine columns

Site
  Number of sites in alignment

Neutral
  (minus) Log-probability of observing site given that it was 
  evolving neutrally (omega=1)

Optimal
  (minus) Log-probability of observing site given that it was 
  evolving at the optimal value of omega.

Omega
  The value of omega which maximizes the log-probability of observing

LRT_Stat
  Log-likelihood ratio statistic for non-neutral selection (or
  positive selection if the positive_only option is set to 1).
  LRT_Stat = 2 * (Neutral-Optimal)

Pval
  P-value for non-neutral (or positive) selection at a site,
  unadjusted for multiple comparisons.

Adj. Pval
  P-value for non-neutral (or positive) selection at a site, after
  adjusting for multiple comparisons using the Hochberg procedure 
  (see the file ``MultipleComparisons.txt'' in the doc directory).

Result
  A simple visual guide to the result. Sites detected as having been
  under positive selection are marked with a '+', sites under 
  purifying selection are marked with '-'. The number of symbols
    Number symbols      Threshold
          1             95%
          2             99%
          3             95% after adjustment
          4             99% after adjustment

   Occasionally the result may also contain an exclamation mark. This
   indicates that the observation at a site is not significantly
   different from random (equivalent to infinitely strong positive
   selection). This may indicate that the alignment at that site is bad
 
 

Note

   The following events are flagged:
   Synonymous            All codons at a site code for the same amino 
                         acid.
   Single character      Only one sequence at the site is ungapped,
                         the result of a recent insertion for example.
   All gaps              All sequences at a site contain a gap
                         character.
 
   Sites marked "Single character" or "All gaps" are not counted
   towards the number of sites for the purposes of correcting for
   multiple comparisons since it is not possible to detect selection
   from none or one observation under the assumptions made by the
   sitewise likelihood ratio test.
 
 

program_name

  Title   : program_name
  Usage   : $factory->program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : ->program_dir()
  Function: returns the program directory, obtained from ENV variable.
  Returns:  string
  Args    :
 
 

new

  Title   : new
  Usage   : my $obj = Bio::Tools::Run::Phylo::SLR->new();
  Function: Builds a new Bio::Tools::Run::Phylo::SLR object 
  Returns : Bio::Tools::Run::Phylo::SLR
  Args    : -alignment => the Bio::Align::AlignI object
            -save_tempfiles => boolean to save the generated tempfiles and
                               NOT cleanup after onesself (default FALSE)
            -tree => the Bio::Tree::TreeI object
            -params => a hashref of SLR parameters (all passed to set_parameter)
            -executable => where the SLR executable resides
 
 

See also: Bio::Tree::TreeI, Bio::Align::AlignI

prepare

  Title   : prepare
  Usage   : my $rundir = $slr->prepare($aln);
  Function: prepare the SLR analysis using the default or updated parameters
            the alignment parameter must have been set
  Returns : value of rundir
  Args    : L<Bio::Align::AlignI> object,
            L<Bio::Tree::TreeI> object
 
 

run

  Title   : run
  Usage   : my ($rc,$parser) = $slr->run($aln,$tree);
  Function: run the SLR analysis using the default or updated parameters
            the alignment parameter must have been set
  Returns : Return code, L<Bio::Tools::Phylo::SLR>
  Args    : L<Bio::Align::AlignI> object,
            L<Bio::Tree::TreeI> object
 
 

error_string

  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)
 
 

alignment

  Title   : alignment
  Usage   : $slr->align($aln);
  Function: Get/Set the L<Bio::Align::AlignI> object
  Returns : L<Bio::Align::AlignI> object
  Args    : [optional] L<Bio::Align::AlignI>
  Comment : We could potentially add support for running directly on a file
            but we shall keep it simple
  See also: L<Bio::SimpleAlign>
 
 

tree

  Title   : tree
  Usage   : $slr->tree($tree, %params);
  Function: Get/Set the L<Bio::Tree::TreeI> object
  Returns : L<Bio::Tree::TreeI> 
  Args    : [optional] $tree => L<Bio::Tree::TreeI>,
 
  Comment : We could potentially add support for running directly on a file
            but we shall keep it simple
  See also: L<Bio::Tree::Tree>
 
 

get_parameters

  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_parameter

  Title   : set_parameter
  Usage   : $slr->set_parameter($param,$val);
  Function: Sets a SLR parameter, will be validated against
            the valid values as set in the %VALIDVALUES class variable.  
            The checks can be ignored if one turns off param checks like this:
              $slr->no_param_checks(1)
  Returns : boolean if set was success, if verbose is set to -1
            then no warning will be reported
  Args    : $param => name of the parameter
            $value => value to set the parameter to
  See also: L<no_param_checks()>
 
 

set_default_parameters

  Title   : set_default_parameters
  Usage   : $slr->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
 
 

Bio::Tools::Run::WrapperBase methods

no_param_checks

  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_tempfiles

  Title   : save_tempfiles
  Usage   : $obj->save_tempfiles($newval)
  Function: 
  Returns : value of save_tempfiles
  Args    : newvalue (optional)
 
 

outfile_name

  Title   : outfile_name
  Usage   : my $outfile = $slr->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
 
 

tempdir

  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
 
 

cleanup

  Title   : cleanup
  Usage   : $slr->cleanup();
  Function: Will cleanup the tempdir directory after an SLR run
  Returns : none
  Args    : none
 
 

io

  Title   : io
  Usage   : $obj->io($newval)
  Function:  Gets a L<Bio::Root::IO> object
  Returns : L<Bio::Root::IO>
  Args    : none