added prefix option to write_fasta_files and write_fastq_files

[biopieces.git] / bp_bin / write_fastq_files

diff --git a/bp_bin/write_fastq_files b/bp_bin/write_fastq_files
index 5e36a38eb44134c1d024c5d1467e0cb212aaf91a..b475b121eeec6cead74d03a9c767023d640870ef 100755 (executable)
--- a/bp_bin/write_fastq_files
+++ b/bp_bin/write_fastq_files
@@ -37,6 +37,7 @@ 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: '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}
@@ -59,7 +60,12 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       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")
+        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)