require 'maasha/fastq'
require 'pp'
+allowed_enc = 'base_33,base_64'
+
casts = []
-casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'dir', :short=>'d', :type=>'dir!', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'dir', :short=>'d', :type=>'dir!', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'base_33', :allowed=>allowed_enc, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
+encoding = options[:encoding].to_sym
+
key = options[:key].to_sym
fh_hash = {}
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES] and record[key]
- seq = Seq.new_bp(record)
+ entry = Seq.new_bp(record)
+ entry.qual_convert!(:base_33, encoding)
- if fh_hash.has_key? record[key].to_sym
+ if fh_hash[record[key].to_sym]
fastq_io = fh_hash[record[key].to_sym]
else
fastq_file = File.join(options[:dir], record[key] + ".fastq")
fh_hash[record[key].to_sym] = fastq_io
end
- fastq_io.puts seq.to_fastq
+ fastq_io.puts entry.to_fastq
end
output.puts record unless options[:no_stream]