3 # Copyright (C) 2007-2011 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Find barcodes in sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
35 # Hard coded Roche Genome Sequencing MIDs
192 # Hard coded Roche Rapid Labrary MIDs
246 class BarCodeFinderError < StandardError; end
249 def initialize(pos, max_mismatches)
251 @max_mismatches = max_mismatches
256 def parse_barcodes(file)
260 File.open(file, "r") do |ios|
262 name, barcode = ios.readline.chomp.split(/\s+/)
265 raise BarCodeFinderError, "Uneven barcode length detected" if length != barcode.length
267 length = barcode.length
270 hash[barcode.upcase.to_sym] = name
277 def load_barcodes(hash)
278 @barcode_sizes << hash.keys.first.to_s.size
280 @barcode_hash.merge!(hash)
283 def find_barcode(seq)
284 raise BarCodeFinderError, "No barcodes to find" if @barcode_hash.empty?
286 @barcode_sizes.each do |size|
288 barcode = seq[@pos ... @pos + size].upcase.to_sym
290 if @barcode_hash.has_key? barcode
291 return BarCode.new(barcode, @barcode_hash[barcode], @pos, size, hamming_dist)
292 elsif @max_mismatches > 0
293 @barcode_hash.each_key do |key|
294 if key.to_s.length == barcode.to_s.size
295 hamming_dist = barcode.to_s.hamming_distance(key.to_s)
297 if hamming_dist <= @max_mismatches
298 return BarCode.new(key, @barcode_hash[key], @pos, size, hamming_dist)
310 # Class to hold a BacCode object.
312 attr_accessor :barcode, :name, :pos, :len, :mismatches
314 def initialize(barcode, name, pos, len, mismatches)
319 @mismatches = mismatches
324 hash[:BARCODE] = @barcode
325 hash[:BARCODE_NAME] = @name
326 hash[:BARCODE_POS] = @pos
327 hash[:BARCODE_LEN] = @len
328 hash[:BARCODE_MISMATCHES] = @mismatches
339 casts << {:long=>'barcodes_in', :short=>'b', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
340 casts << {:long=>'pos', :short=>'p', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
341 casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>"0,1,2", :disallowed=>nil}
342 casts << {:long=>'gsmids', :short=>'g', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
343 casts << {:long=>'rlmids', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
344 casts << {:long=>'remove', :short=>'R', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
346 options = Biopieces.options_parse(ARGV, casts)
348 bc_finder = BarCodeFinder.new(options[:pos], options[:mismatches])
349 bc_finder.parse_barcodes(options[:barcodes_in]) if options[:barcodes_in]
350 bc_finder.load_barcodes(GSMID_HASH) if options[:gsmids]
351 bc_finder.load_barcodes(RLMID_HASH) if options[:rlmids]
353 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
354 input.each_record do |record|
355 if record.has_key? :SEQ
356 if barcode = bc_finder.find_barcode(record[:SEQ])
357 record.merge!(barcode.to_hash)
360 record[:SEQ] = record[:SEQ][barcode.start .. -1]
361 record[:SCORES] = record[:SCORES][barcode.start .. -1] if record[:SCORES]
362 record[:SEQ_LEN] = record[:SEQ].length
372 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<