#!/usr/bin/env ruby
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2013 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fastq'
+require 'maasha/biopieces'
+require 'maasha/fastq'
-casts = []
-casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'solexa', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+MAX_TEST = 1_000
-PHRED_SCORES = Regexp.new('[!"#$%&\'()*+,-./0123456789:]')
+allowed_enc = 'auto,base_33,base_64'
-bp = Biopieces.new
+casts = []
+casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'data_in2', :short=>'j', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'auto', :allowed=>allowed_enc, :disallowed=>nil}
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
-bp.each_record do |record|
- bp.puts record
-end
+encoding = options[:encoding].to_sym
num = 0
last = false
-if options.has_key? :data_in
- options[:data_in].each do |file|
- Fastq.open(file, mode='r') do |fastq|
- fastq.each do |entry|
- entry.convert_phred2illumina! if entry.qual.match PHRED_SCORES
- entry.convert_solexa2illumina! if options[:solexa]
- bp.puts entry.to_bp
- num += 1
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ unless options[:data_in] and options[:data_in].first == '-'
+ input.each_record do |record|
+ output.puts record
+ end
+ end
+
+ if options[:data_in] and options[:data_in2]
+ raise "data_in files differ" if options[:data_in].size != options[:data_in2].size
+
+ (0 ... options[:data_in].size).each do |i|
+ file1 = options[:data_in][i]
+ file2 = options[:data_in2][i]
+
+ io1 = Fastq.open(file1, 'r')
+ io2 = Fastq.open(file2, 'r')
+
+ while not io1.eof? and not io2.eof?
+ entry1 = io1.get_entry
+ entry2 = io2.get_entry
+
+ if encoding == :auto
+ if entry1.qual_base33? or entry2.qual_base33?
+ encoding = :base_33
+ elsif entry1.qual_base64? or entry2.qual_base64?
+ encoding = :base_64
+ else
+ raise SeqError, "Could not auto-detect quality score encoding"
+ end
+ end
- if options.has_key? :num and options[:num] == num
+ entry1.qual_convert!(encoding, :base_33)
+ entry2.qual_convert!(encoding, :base_33)
+ entry1.qual_coerce!(:base_33)
+ entry2.qual_coerce!(:base_33)
+
+ if num < MAX_TEST
+ raise SeqError, "Quality score outside valid range" unless entry1.qual_valid?(:base_33)
+ raise SeqError, "Quality score outside valid range" unless entry2.qual_valid?(:base_33)
+ end
+
+ output.puts entry1.to_bp
+ output.puts entry2.to_bp
+
+ num += 2
+
+ if options[:num] and num >= options[:num]
last = true
break
end
end
+
+ io1.close
+ io2.close
+
+ break if last
end
+ elsif options[:data_in]
+ options[:data_in].each do |file|
+ Fastq.open(file, 'r') do |fastq|
+ fastq.each do |entry|
+ if encoding == :auto
+ if entry.qual_base33?
+ encoding = :base_33
+ elsif entry.qual_base64?
+ encoding = :base_64
+ else
+ raise SeqError, "Could not auto-detect quality score encoding"
+ end
+ end
+
+ entry.qual_convert!(encoding, :base_33)
+ entry.qual_coerce!(:base_33)
+
+ if num < MAX_TEST
+ raise SeqError, "Quality score outside valid range" unless entry.qual_valid?(:base_33)
+ end
+
+ output.puts entry.to_bp
+ num += 1
+
+ if options[:num] == num
+ last = true
+ break
+ end
+ end
+ end
- break if last
+ break if last
+ end
end
end