module Neurohmmer

Top level module / namespace.

Constants

VERSION

Attributes

conf[RW]

opt[RW]

Public Class Methods

extract_sequence(id) click to toggle source

# File lib/neurohmmer.rb, line 36
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) click to toggle source

# 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",
    fasta_output: "#{@opt[:input_file]}.neurohmmer.fa"
  }
  init_input
end

run() click to toggle source

# File lib/neurohmmer.rb, line 28
def run
  Hmmer.search
  hmm_analysis = Hmmer.analyse_output
  Output.to_fasta(hmm_analysis)
  Output.to_html(hmm_analysis)
  remove_temp_dir
end

Private Class Methods

index(content, keys, values) click to toggle source

A method run from index_input_file that creates a simple hash with the {seq id: [start byte in file, end byte in file] }

# File lib/neurohmmer.rb, line 76
def index(content, keys, values)
  fasta_index = {}
  keys.each_with_index do |k, i|
    id = k[0..115].gsub(/\s+/, '')
    endf  = (i == values.length - 1) ? content.length - 1 : values[i + 1]
    fasta_index[id] = [values[i], endf]
  end
  fasta_index
end

index_input_file() click to toggle source

Indexes the input file - returns a hash in the following format: {seq id: [start byte in file, end byte in file] }

# File lib/neurohmmer.rb, line 67
def index_input_file
  c = IO.binread(@opt[:input_file])
  keys   = c.scan(/>(.*)\n/).flatten
  values = c.enum_for(:scan, /(>[^>]+)/).map { Regexp.last_match.begin(0) }
  index(c, keys, values)
end

init_input() click to toggle source

# File lib/neurohmmer.rb, line 45
def init_input
  FileUtils.mkdir_p(@opt[:temp_dir])
  @opt[:input_file] = translate_input if @opt[:type] == :genetic
  @input_index = index_input_file
end

remove_temp_dir() click to toggle source

# File lib/neurohmmer.rb, line 86
def remove_temp_dir
  return unless File.directory?(@opt[:temp_dir])
  FileUtils.rm_rf(@opt[:temp_dir])
end

translate_input(input = @opt[:input_file]) click to toggle source

Translates the input data in all 6 frames

# File lib/neurohmmer.rb, line 52
def translate_input(input = @opt[:input_file])
  translated_file = File.join(@opt[:temp_dir], 'input.translated.fa')
  File.open(translated_file, 'w') do |file|
    Bio::FlatFile.open(Bio::FastaFormat, input).each_entry do |entry|
      (1..6).each do |f|
        file.puts ">#{entry.definition}-frame:#{f}"
        file.puts entry.naseq.translate(f)
      end
    end
  end
  translated_file
end