[med-svn] [Git][med-team/python-treetime][upstream] New upstream version 0.8.1

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / python-treetime


Commits:
28bc86c7 by Nilesh Patra at 2021-01-09T16:15:26+05:30
New upstream version 0.8.1
- - - - -


4 changed files:

- changelog.md
- treetime/__init__.py
- treetime/seq_utils.py
- treetime/treeanc.py


Changes:

=====================================
changelog.md
=====================================
@@ -1,3 +1,5 @@
+# 0.8.1 -- bug fixe amino acid profile map.
+
 # 0.8.0 -- drop python 2.7 support, bug fixes.
 
 # 0.7.6 -- catch of distributions are too short for calculating confidence intervals.


=====================================
treetime/__init__.py
=====================================
@@ -1,5 +1,5 @@
 from __future__ import print_function, division, absolute_import
-version="0.8.0"
+version="0.8.1"
 
 class TreeTimeError(Exception):
     """TreeTimeError class"""


=====================================
treetime/seq_utils.py
=====================================
@@ -83,7 +83,7 @@ profile_maps = {
     'V': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], dtype='float'), #Valine          Val
     'W': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], dtype='float'), #Tryptophan      Trp
     'Y': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], dtype='float'), #Tyrosine        Tyr
-    '*': np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0], dtype='float'), #stop
+    '*': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], dtype='float'), #stop
     '-': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1], dtype='float'), #gap
     'X': np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype='float'), #not specified/any
     'B': np.array([0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float'), #Asparagine/Aspartic Acid    Asx


=====================================
treetime/treeanc.py
=====================================
@@ -1611,8 +1611,10 @@ class TreeAnc(object):
         else:
             if (not reconstructed) and (node.name in self.data.aln):
                 tmp_seq = self.data.aln[node.name]
-            else:
+            elif node.cseq is not None:
                 tmp_seq = self.data.compressed_to_full_sequence(node.cseq, as_string=False)
+            else:
+                tmp_seq = np.array([self.gtr.ambiguous or 'N']*self.data.compressed_length)
 
         return "".join(tmp_seq) if as_string else np.copy(tmp_seq)
 



View it on GitLab: https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986

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View it on GitLab: https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986
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