Class | Bio::PAML::Yn00 |
In: |
lib/bio/appl/paml/yn00.rb
lib/bio/appl/paml/yn00/report.rb |
Parent: | Common |
Bio::PAML::Yn00 is a wrapper for running PAML yn00 program.
Because most of the methods in this class are inherited from Bio::PAML::Common, see documents of Bio::PAML::Common for details.
Example 1:
require 'bio' # Reads multi-fasta formatted file and gets a Bio::Alignment object. alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat, 'example.fst').alignment # Creates a Yn00 object baseml = Bio::PAML::Yn00.new # Sets parameters baseml.parameters[:verbose] = 1 baseml.parameters[:icode] = 0 # You can also set many parameters at a time. baseml.parameters.update({ :weighting => 0, :commonf3x4 => 0 }) # Executes yn00 with the alignment report = yn00.query(alignment)
DEFAULT_PROGRAM | = | 'yn00'.freeze | Default program name | |
DEFAULT_PARAMETERS | = | { # Essential argumemts :seqfile => nil, :outfile => nil, # Optional arguments :verbose => 1, :icode => 0, :weighting => 0, :commonf3x4 => 0 |
Default parameters when running baseml.
The parameters whose values are different from the baseml defalut value (described in pamlDOC.pdf) in PAML 4.1 are: seqfile, outfile, treefile, ndata, noisy, verbose |
Runs the program on the internal parameters with the specified sequence alignment. Note that parameters[:seqfile] and parameters[:outfile] are always modified.
For other important information, see the document of Bio::PAML::Common#query.
Arguments:
Returns: | Report object |
# File lib/bio/appl/paml/yn00.rb, line 83 83: def query(alignment) 84: super(alignment) 85: end
Runs the program on the internal parameters with the specified sequence alignment as a String object.
For other important information, see the document of query and Bio::PAML::Common#query_by_string methods.
Arguments:
Returns: | Report object |
# File lib/bio/appl/paml/yn00.rb, line 97 97: def query_by_string(alignment = nil) 98: super(alignment) 99: end