adding bzip2 support in ruby

[biopieces.git] / bp_bin / write_fastq

diff --git a/bp_bin/write_fastq b/bp_bin/write_fastq
index f6050f38555071932cab4ad91eaba821c8d84a83..d15c96f9dd31eb0ac6792b6b70d092ddcdd29bb6 100755 (executable)
--- a/bp_bin/write_fastq
+++ b/bp_bin/write_fastq
@@ -31,41 +31,36 @@
 require 'maasha/biopieces'
 require 'maasha/fastq'
 
-allowed_enc = 'sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
+allowed_enc = 'base_33,base_64'
 
 casts = []
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,           :allowed=>nil,         :disallowed=>nil}
-casts << {:long=>'data_out',  :short=>'o', :type=>'file',   :mandatory=>false, :default=>nil,           :allowed=>nil,         :disallowed=>nil}
-casts << {:long=>'encoding',  :short=>'e', :type=>'string', :mandatory=>false, :default=>'illumina1.3', :allowed=>allowed_enc, :disallowed=>nil}
-casts << {:long=>'compress',  :short=>'Z', :type=>'flag',   :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: 'data_out',  short: 'o', type: 'file',   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}
+casts << {long: 'compress',  short: 'Z', type: 'string', mandatory: false, default: nil,       allowed: "gzip,bzip,bzip2", disallowed: nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-encoding = options[:encoding].downcase.delete('.')
+encoding = options[:encoding].to_sym
+compress = options[:compress] ? options[:compress].to_sym : nil
+
+raise "--data_out is mandatory for compressed output" if compress and not options[:data_out]
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  if options[:data_out]
-    if options[:compress]
-      io_out = Zlib::GzipWriter.open(options[:data_out])
-    else
-      io_out = Fastq.open(options[:data_out], 'w')
-    end
-  else
-    io_out = $stdout
-  end
+  fastq_out = options[:data_out] ? Fastq.open(options[:data_out], 'w', compress: compress) : STDOUT
 
   input.each do |record|
     if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
       entry = Seq.new_bp(record)
-      entry.convert_scores!('illumina13', encoding)
+      entry.qual_convert!(:base_33, encoding)
 
-      io_out.puts entry.to_fastq
+      fastq_out.puts entry.to_fastq
     end
 
-    output.puts record unless options.has_key? :no_stream
+    output.puts record unless options[:no_stream]
   end
 
-  io_out.close
+  fastq_out.close
 end