Changeset 5747

Timestamp:

Nov 21, 2019, 8:40:55 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

Fixes an issue with missing "N" values in the lookup tables for GC content and DNA strength.

File:

• other/pipeline/trunk/gc_stat.py (modified) (1 diff)

other/pipeline/trunk/gc_stat.py

@@ -41 +41 @@
 
 # GC content and DNA strength values
-GC_CONT_VALUES = { "A": 0.0, "C": 1.0, "G": 1.0, "T": 0.0 }
+GC_CONT_VALUES = { "A": 0.0, "C": 1.0, "G": 1.0, "N": 0.5, "T": 0.0 }
 DNA_STRENGTH_VALUES = {
-    "AA": 5.0, "AC": 10.0, "AG": 8.0, "AT": 7.0,
-    "CA": 7.0, "CC": 11.0, "CG": 10.0, "CT": 8.0, 
-    "GA": 8.0, "GC": 13.0, "GG": 11.0, "GT": 10.0,
-    "TA": 4.0, "TC": 8.0, "TG": 7.0, "TT": 5.0
+    "AA": 5.0, "AC": 10.0, "AG": 8.0, "AN": 7.5, "AT": 7.0,
+    "CA": 7.0, "CC": 11.0, "CG": 10.0, "CN": 9.0, "CT": 8.0, 
+    "GA": 8.0, "GC": 13.0, "GG": 11.0, "GN": 10.5, "GT": 10.0,
+    "NA": 6.0, "NC": 10.5, "NG": 9.0, "NN": 8.25, "NT": 7.5,
+    "TA": 4.0, "TC": 8.0, "TG": 7.0, "TN": 6.0, "TT": 5.0
   }