updated RSCU function based on issue #6

JLSteenwyk · Jun 12, 2024 · 05408ad · 05408ad
1 parent 595a79d
commit 05408ad
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Showing 5 changed files with 19 additions and 14 deletions.
diff --git a/biokit/services/coding_sequences/base.py b/biokit/services/coding_sequences/base.py
@@ -57,7 +57,7 @@ def calculate_rscu(self, translation_table) -> dict:
                 try:
                     observed_sum += codon_counts[codon]
                 except KeyError:
-                    observed_sum = 0
+                    pass
             for codon in codons:
                 try:
                     rscu[codon] = round(

diff --git a/biokit/version.py b/biokit/version.py
@@ -1 +1 @@
-__version__ = "1.1.2"
+__version__ = "1.1.3"
diff --git a/change_log.txt b/change_log.txt
@@ -21,3 +21,6 @@ Added "X" as a gap character during alignment recoding
 
 1.1.0
 Added Dayhoff-9, -12, -15, and -18 recoding schemes 
+
+1.1.3
+Fixed bug in RSCU calculations
diff --git a/docs/change_log/index.rst b/docs/change_log/index.rst
@@ -25,3 +25,5 @@ are skipped during analysis of RSCU and gw-RSCU.
 *1.0.1*: Added "X" as a gap character during alignment recoding
 
 *1.1.0*: Added Dayhoff-9, -12, -15, and -18 recoding schemes 
+
+*1.1.3*: Fixed bug in RSCU calculations
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,3 +21,6 @@ Added "X" as a gap character during alignment recoding @@
 .1.0
     Added Dayhoff-9, -12, -15, and -18 recoding schemes
+.1.3
+    Fixed bug in RSCU calculations
Original file line number	Diff line number	Diff line change
Expand Up		@@ -25,3 +25,5 @@ are skipped during analysis of RSCU and gw-RSCU.
		1.0.1: Added "X" as a gap character during alignment recoding

		1.1.0: Added Dayhoff-9, -12, -15, and -18 recoding schemes

		1.1.3: Fixed bug in RSCU calculations