Class: Bio::TMHMM::TmHmmWrapper
- Inherits:
-
Object
- Object
- Bio::TMHMM::TmHmmWrapper
- Defined in:
- lib/bio/appl/tmhmm/tmhmm_runner.rb
Instance Method Summary collapse
-
#calculate(sequence) ⇒ Object
Given an amino acid sequence, return a TransmembraneProtein made up of the predicted transmembrane domains.
Instance Method Details
#calculate(sequence) ⇒ Object
Given an amino acid sequence, return a TransmembraneProtein made up of the predicted transmembrane domains
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# File 'lib/bio/appl/tmhmm/tmhmm_runner.rb', line 8 def calculate(sequence) Bio::Command.mktmpdir do |d| line = nil Bio::Command.call_command(['tmhmm','-short'], :chdir => d) do |io| io.puts '>wrapperSeq' io.puts sequence io.close_write line = io.readline end if line.nil? raise Exception, "Error running locally installed TMHMM program 'tmhmm'. Is it properly installed?" end return TmHmmResult.create_from_short_line(line) end end |