added prefix option to write_fasta_files and write_fastq_files

[biopieces.git] / bp_bin / write_fasta_files

diff --git a/bp_bin/write_fasta_files b/bp_bin/write_fasta_files
index a0e20a50545643b2183ee2fdf229ba08ab2d68df..dfeabb20a5555517af240461eb574cb79ed2f125 100755 (executable)
--- a/bp_bin/write_fasta_files
+++ b/bp_bin/write_fasta_files
@@ -35,6 +35,7 @@ require 'pp'
 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: 'wrap',      short: 'w', type: 'uint',   mandatory: false, default: nil, allowed: nil,               disallowed: "0"}
 casts << {long: 'compress',  short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
 casts << {long: 'no_stream', short: 'x', type: 'flag',   mandatory: false, default: nil, allowed: nil,               disallowed: nil}
@@ -53,7 +54,12 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       if fh_hash[record[key].to_sym]
         fasta_io = fh_hash[record[key].to_sym]
       else
-        fasta_file = File.join(options[:dir], record[key] + ".fasta")
+        if options[:prefix]
+          fasta_file = File.join(options[:dir], [options[:prefix], record[key]].join("_") + ".fasta")
+        else
+          fasta_file = File.join(options[:dir], record[key] + ".fasta")
+        end
+
         fasta_file << ".gz"  if compress == :gzip
         fasta_file << ".bz2" if compress == :bzip or compress == :bzip2
         fasta_io   = Fasta.open(fasta_file, "w", compress: compress)