add tests for analyze_seq

[biopieces.git] / bp_bin / analyze_seq

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
index 81ad0e16aa20393fad2662eb930c950e97d81822..f79d94a92134882b25584e65feccaccfc4be9882 100755 (executable)
--- a/bp_bin/analyze_seq
+++ b/bp_bin/analyze_seq
@@ -31,6 +31,7 @@
 
 require 'biopieces'
 require 'seq'
+require 'pp'
 
 casts = []
 
@@ -44,18 +45,19 @@ bp.each_record do |record|
     comp = seq.composition
 
     comp.each_pair do |key,val|
-      record["RES_#{key}"] = val
+      record["RES[#{key}]"] = val
     end
 
-    record["HARD_MASK"] = seq.hard_mask
-    record["SOFT_MASK"] = seq.soft_mask
-    record["GC"]        = ((comp["G"] + comp["C"]).to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+    record["SOFT_MASK%"] = seq.soft_mask
+    record["HARD_MASK%"] = (comp["N"].to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+    record["GC%"]        = ((comp["G"] + comp["C"]).to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
   end
 
   bp.puts record
 end
 
 
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<