Class: Basil::Basil

Inherits:
Object
  • Object
show all
Defined in:
lib/basil/basil.rb

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(barcodes) ⇒ Basil

Gets Basil ready, must specify a barcodes hash with Basil.new barcodes

Barcodes hash has regexp for values. If not, strings are converted to regexp Barcode names are keys, used to generate filenames.



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

def initialize(barcodes)
  @barcodes = Hash.new
  barcodes.each_pair do |k, v|
    @barcodes[k] = Regexp.new "^#{v}", true
  end
  @barcodes
end

Class Method Details

.parse_barcodes(handle, args = {}) ⇒ Object

Parses a barcodes file

barcodes are specified in CSV file (unless specified otherwise with :sep => ”) barcode_name,sequence the barcode_name will be used to generate the filename



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# File 'lib/basil/basil.rb', line 52

def self.parse_barcodes(handle, args={})
  sep = args[:sep] || ","
  barcodes = handle.each.collect do |line|
    name, barcode = line.strip.split(sep)
  end
  Hash[*barcodes.flatten]
end

Instance Method Details

#recognize(string) ⇒ Object

Finds the barcode (if present)

If the barcode is present, returns ‘name’, and the sequence with the barcode removed If not, returns nil



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# File 'lib/basil/basil.rb', line 26

def recognize(string)
  matches = @barcodes.each_pair.collect do |k, v|
    k if string[v]
  end

  matches.compact!

  if matches.length > 1
    raise Exception, "sequence #{string} has more than one match"
  elsif matches.length == 0
    nil
  else
    barcode = matches.first
    sequence = string.gsub(@barcodes[barcode], '')
    [barcode, sequence]
  end
end