Class: Bio::Velvet::Result

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-velvet/runner.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#result_directory ⇒ Object

Returns the value of attribute result_directory.



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# File 'lib/bio-velvet/runner.rb', line 86

def result_directory
  @result_directory
end

#velvetg_stderr ⇒ Object

Returns the value of attribute velvetg_stderr.



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# File 'lib/bio-velvet/runner.rb', line 85

def velvetg_stderr
  @velvetg_stderr
end

#velvetg_stdout ⇒ Object

Returns the value of attribute velvetg_stdout.



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# File 'lib/bio-velvet/runner.rb', line 85

def velvetg_stdout
  @velvetg_stdout
end

#velveth_stderr ⇒ Object

Returns the value of attribute velveth_stderr.



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# File 'lib/bio-velvet/runner.rb', line 84

def velveth_stderr
  @velveth_stderr
end

#velveth_stdout ⇒ Object

Returns the value of attribute velveth_stdout.



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# File 'lib/bio-velvet/runner.rb', line 84

def velveth_stdout
  @velveth_stdout
end

Instance Method Details

#contigs_path ⇒ Object

Path to the contigs.fa output from velvetg



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# File 'lib/bio-velvet/runner.rb', line 94

def contigs_path
  File.join result_directory, 'contigs.fa'
end

#last_graph(options = nil) ⇒ Object

Return a Bio::Velvet::Graph object built from the LastGraph file. The options for parsing are as per Bio::Velvet::Graph#parse_from_file



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# File 'lib/bio-velvet/runner.rb', line 105

def last_graph(options=nil)
  Bio::Velvet::Graph.parse_from_file(last_graph_path, options)
end

#last_graph_path ⇒ Object

Path to the LastGraph output from velvetg



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# File 'lib/bio-velvet/runner.rb', line 89

def last_graph_path
  File.join result_directory, 'LastGraph'
end

#stats_path ⇒ Object

Path to the stats.txt output from velvetg



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# File 'lib/bio-velvet/runner.rb', line 99

def stats_path
  File.join result_directory, 'stats.txt'
end