added -o and -x to analyze_vals

[biopieces.git] / bp_bin / analyze_vals

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index e7e8249a8faf73c53bce080d333e56a73a2b7aa1..951f321f808e7b4e907d11d791e29c37cb1d64c2 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -31,8 +31,10 @@
 require 'maasha/biopieces'
 
 casts = []
-casts << {long: 'keys',    short: 'k', type: 'list', mandatory: false, default: nil, allowed: nil, disallowed: nil}
-casts << {long: 'no_keys', short: 'K', type: 'list', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'keys',      short: 'k', type: 'list', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'no_keys',   short: 'K', type: 'list', 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}
 
 options = Biopieces.options_parse(ARGV, casts)
 
@@ -91,6 +93,12 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
       stats[key][:count] += 1
     end
+
+    output.puts record unless options[:no_stream]
+  end
+
+  if options[:data_out]
+    data_out = File.open(options[:data_out], 'w')
   end
 
   stats.each do |key, value|
@@ -104,7 +112,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       :MEAN  => "%0.2f" % (value[:sum] / value[:count].to_f)
     }
 
-    output.puts stat_record
+    if options[:data_out]
+      data_out.puts stat_record
+    else
+      output.puts stat_record
+    end
   end
 end