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: 'prefix', short: 'p', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'no_stream', short: 'x', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'compress', short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", 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
+compress = options[:compress] ? options[:compress].to_sym : nil
+
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[record[key].to_sym]
fastq_io = fh_hash[record[key].to_sym]
else
- fastq_file = File.join(options[:dir], record[key] + ".fastq")
- fastq_io = Fastq.open(fastq_file, "w")
+ if options[:prefix]
+ fastq_file = File.join(options[:dir], [options[:prefix], record[key]].join("_") + ".fastq")
+ else
+ fastq_file = File.join(options[:dir], record[key] + ".fastq")
+ end
+
+ fastq_file << ".gz" if compress == :gzip
+ fastq_file << ".bz2" if compress == :bzip or compress == :bzip2
+ fastq_io = Fastq.open(fastq_file, "w", compress: compress)
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]