Module: Neurohmmer

Defined in:
lib/neurohmmer.rb,
lib/neurohmmer/hmmer.rb,
lib/neurohmmer/output.rb,
lib/neurohmmer/signalp.rb,
lib/neurohmmer/version.rb,
lib/neurohmmer/arg_validators.rb

Overview

Top level module / namespace.

Defined Under Namespace

Classes: ArgumentsValidators, Hmmer, Output, Signalp

Constant Summary collapse

VERSION = 
'0.1.1'

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.conf ⇒ Object

Returns the value of attribute conf.



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# File 'lib/neurohmmer.rb', line 12

def conf
  @conf
end

.opt ⇒ Object

Returns the value of attribute opt.



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# File 'lib/neurohmmer.rb', line 11

def opt
  @opt
end

Class Method Details

.extract_sequence(id) ⇒ Object 



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# File 'lib/neurohmmer.rb', line 34

def extract_sequence(id)
  id = id.gsub(/\s+/, '')
  idx = @input_index[id]
  seq = IO.binread(@opt[:input_file], idx[1] - idx[0], idx[0])
  seq.scan(/>([^\n]*)\n([A-Za-z\n\*]*)/)[0]
end

.init(opt) ⇒ Object 



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# File 'lib/neurohmmer.rb', line 14

def init(opt)
  @opt = ArgumentsValidators.run(opt)
  @conf = {
    hmm_dir: File.expand_path('../../data/hmm', __FILE__),
    raw_data: File.expand_path('../../data/raw_data', __FILE__),
    raw_alignments: File.expand_path('../../data/raw_data/alignments',
                                     __FILE__),
    hmm_output: File.join(@opt[:temp_dir], 'input.hmm_search.out'),
    html_output: "#{@opt[:input_file]}.neurohmmer.html"
  }
  init_input
end

.run ⇒ Object 



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# File 'lib/neurohmmer.rb', line 27

def run
  Hmmer.search
  hmm_analysis = Hmmer.analyse_output
  Output.to_html(hmm_analysis)
  remove_temp_dir
end