class Bio::PAML::Codeml::ReportSingle
ReportSingle is a simpler parser for a codeml report containing a single run. This is retained for backward compatibility mostly.
The results of a single model (old style report parser)
>> single = Bio::PAML::Codeml::Report.new(buf) >> single.tree_log_likelihood => -1817.465211 >> single.tree_length => 0.77902 >> single.alpha => 0.58871 >> single.tree => "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
Attributes
alpha[R]
tree[R]
tree_length[R]
tree_log_likelihood[R]
Public Class Methods
new(codeml_report)
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# File lib/bio/appl/paml/codeml/report.rb, line 367 def initialize(codeml_report) @tree_log_likelihood = pull_tree_log_likelihood(codeml_report) @tree_length = pull_tree_length(codeml_report) @alpha = pull_alpha(codeml_report) @tree = pull_tree(codeml_report) end
Private Instance Methods
pull_alpha(text)
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# File lib/bio/appl/paml/codeml/report.rb, line 387 def pull_alpha(text) text[/alpha .+ =\s+(-?\d+(\.\d+)?)/,1].to_f end
pull_tree(text)
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# File lib/bio/appl/paml/codeml/report.rb, line 392 def pull_tree(text) text[/([^\n]+)\n\nDetailed/m,1] end
pull_tree_length(text)
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# File lib/bio/appl/paml/codeml/report.rb, line 382 def pull_tree_length(text) text[/tree length\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f end
pull_tree_log_likelihood(text)
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# File lib/bio/appl/paml/codeml/report.rb, line 377 def pull_tree_log_likelihood(text) text[/lnL\(.+\):\s+(-?\d+(\.\d+)?)/,1].to_f end