Module: MutationsCLI

Defined in:
lib/bio-sam-mutation/mutationscli.rb

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.default_species ⇒ Object

Returns the value of attribute default_species.



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 5

def default_species
  @default_species
end

.tag_to_add ⇒ Object

Returns the value of attribute tag_to_add.



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 5

def tag_to_add
  @tag_to_add
end

Class Method Details

.call_mutations(sam, config) ⇒ Object

Returns a MutationArray



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 39

def self.call_mutations sam, config
  unless config[:single_product]
    first_bases = sam.seq[0..config[:start_length]-1].upcase
    config[first_bases] ? config = config[first_bases] : return
  end
  MutationsCLI.call_mutations_given_product sam, config
end

.call_mutations_given_product(sam, config) ⇒ Object 



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 47

def self.call_mutations_given_product sam, config
  # Stop if a search file is specified, and this isn't it.
  return if MutationsCLI.not_included_file?(config, ARGF)
  sam.mutations(config[:offset],config[:length],config[:translation_start])
end

.construct_products(config_hash) ⇒ Object

Allows multiple amplicons to be considered Organises the configuration data by sequence start



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 68

def self.construct_products config_hash
  new_hash = {}
  config_hash[:products].each do |product_name, config|
    new_hash[config[:start]] = config
    new_hash[config[:start]][:output] ||= product_name + ".sam"
    new_hash[config[:start]][:outfile] = File.open(new_hash[config[:start]][:output],'w')
  end
  lengths = new_hash.keys.map!(&:length).uniq
  new_hash[:start_length] = lengths[0]
  warn "Start sequences given must be same length" if lengths.size > 1
  new_hash
end

.not_included_file?(config, input) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-sam-mutation/mutationscli.rb', line 53

def self.not_included_file? config, input
  config[:file] && input.filename !~ config[:file]
end

.set_defaults(config_hash) ⇒ Object 



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 57

def self.set_defaults config_hash
  config_hash[:start] ||= "." # i.e. regexp will match anything
  config_hash[:offset] ||= 1
  config_hash[:length] ||= 100
  config_hash[:translation_start] ||= 1
  config_hash[:file] = Regexp.new(config_hash[:file]) if config_hash[:file]
  config_hash
end

.tag(sam, config, species = MutationsCLI.default_species) ⇒ Object 



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# File 'lib/bio-sam-mutation/mutationscli.rb', line 8

def self.tag (sam, config, species=MutationsCLI.default_species)
  # With multiple files, could end up with duplicate headers...
  if sam.match(/^@/)
    if config[:single_product]
      config[:outfile].puts sam
      return
    else
      # If we have multiple products, output sam headers to each output file
      config.each do |key, config_hash|
        next if [:start_length].include? key
        config_hash[:outfile].puts sam
      end
      return
    end
  end
  sam = Bio::DB::Alignment.new(sam)
  # DRY up:
  unless config[:single_product]
    first_bases = sam.seq[0..config[:start_length]-1].upcase
    config[first_bases] ? config = config[first_bases] : return
  end
  # Stop if a search file is specified, and this isn't it.
  return if MutationsCLI.not_included_file?(config, ARGF)
  mut_array = sam.mutations(config[:offset],config[:length],config[:translation_start])
  if mut_array
    new_tag = Bio::DB::Tag.new(MutationsCLI.tag_to_add + ":" + mut_array.to_hgvs)
    config[:outfile].puts sam.add_tag(new_tag)
  end
end