Class: ViennaRna::Package::Xbor
- Inherits:
-
Base
- Object
- Base
- ViennaRna::Package::Xbor
show all
- Defined in:
- lib/vienna_rna/package/xbor.rb
Instance Attribute Summary
Attributes inherited from Base
#data, #response, #runtime
Class Method Summary
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Instance Method Summary
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Methods inherited from Base
bootstrap, #debugger, #initialize, #serialize
included
included
Class Method Details
.bootstrap_from_file(path, klass = self) ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 25
def self.bootstrap_from_file(path, klass = self)
log = File.read(path)
sequence = log.split(/\n/).first.split(/\s+/)[1]
structure = log.split(/\n/).first.split(/\s+/)[2]
klass.bootstrap(RNA.from_string(sequence, structure), log)
end
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.parse(response) ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 33
def self.parse(response)
response.split(/\n/).select { |line| line =~ /^\d+\t-?\d+/ }.map { |line| line.split(/\t/) }
end
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Instance Method Details
#expected_k ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 46
def expected_k
k_p_points.map { |array| array.inject(&:*) }.inject(&:+)
end
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#full_distribution ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 37
def full_distribution
distribution = run.distribution
full_distribution = distribution + ([0.0] * ((differnece = data.seq.length - distribution.length + 1) < 0 ? 0 : differnece))
end
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#inspect ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 58
def inspect
"#<#{self.class.name} #{data.inspect}>"
end
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#k_p_points ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 42
def k_p_points
full_distribution.each_with_index.to_a.map(&:reverse)[0..data.seq.length]
end
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#quick_plot(options = {}) ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 50
def quick_plot(options = {})
ViennaRna::Graphing::Gnuplot.quick_plot(
k_p_points,
options[:title] || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure],
options
)
end
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#run_command(flags) ⇒ Object
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# File 'lib/vienna_rna/package/xbor.rb', line 10
def run_command(flags)
file = Tempfile.new("rna")
file.write("%s\n" % data.seq)
file.write("%s\n" % data.str)
file.close
ViennaRna.debugger { "Running FFTbor on #{data.inspect}" }
"%s %s %s" % [
exec_name,
stringify_flags(flags),
file.path
]
end
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