Changeset 5747


Ignore:
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:
1 edited

Legend:

Unmodified
Added
Removed
  • other/pipeline/trunk/gc_stat.py

    r5719 r5747  
    4141
    4242# GC content and DNA strength values
    43 GC_CONT_VALUES = { "A": 0.0, "C": 1.0, "G": 1.0, "T": 0.0 }
     43GC_CONT_VALUES = { "A": 0.0, "C": 1.0, "G": 1.0, "N": 0.5, "T": 0.0 }
    4444DNA_STRENGTH_VALUES = {
    45     "AA": 5.0, "AC": 10.0, "AG": 8.0, "AT": 7.0,
    46     "CA": 7.0, "CC": 11.0, "CG": 10.0, "CT": 8.0,
    47     "GA": 8.0, "GC": 13.0, "GG": 11.0, "GT": 10.0,
    48     "TA": 4.0, "TC": 8.0, "TG": 7.0, "TT": 5.0
     45    "AA": 5.0, "AC": 10.0, "AG": 8.0, "AN": 7.5, "AT": 7.0,
     46    "CA": 7.0, "CC": 11.0, "CG": 10.0, "CN": 9.0, "CT": 8.0,
     47    "GA": 8.0, "GC": 13.0, "GG": 11.0, "GN": 10.5, "GT": 10.0,
     48    "NA": 6.0, "NC": 10.5, "NG": 9.0, "NN": 8.25, "NT": 7.5,
     49    "TA": 4.0, "TC": 8.0, "TG": 7.0, "TN": 6.0, "TT": 5.0
    4950  }
    5051
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