| 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