Merge branch 'griffithlab:master' into master

griffithlab · Nov 3, 2023 · ad86b81 · ad86b81
2 parents 8ce356e + b74da87
commit ad86b81
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diff --git a/docs/conf.py b/docs/conf.py
@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.0.5'
+release = '4.0.6'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

diff --git a/docs/index.rst b/docs/index.rst
@@ -56,15 +56,9 @@ New in Release |release|
 
 This is a bugfix release. It fixes the following problem(s):
 
-- In recent releases, users have noticed that at some point during pipeline
-  runs, predictions to MHCflurry would hang or get killed. We were able to
-  determine that the cause was related to
-  `PR 988 <https://github.com/griffithlab/pVACtools/pull/988>`_.
-  This PR originally updated calls to MHCflurry to happen by instantiating
-  their predictor within Python instead of calling it on the command line.
-  However, we suspect that this causes a substantial increase in memory usage
-  resulting in the observed behavior. This release reverts the change from PR
-  988.
+- A bug in the aggregate report creation incorrectly evaluated the Transcript
+  Support Level and resulted in picking the wrong Best Transcript in some
+  cases.
 
 New in Version |version|
 ------------------------

diff --git a/docs/releases/4_0.rst b/docs/releases/4_0.rst
@@ -1,5 +1,8 @@
-New in Version 4.0.0
---------------------
+Version 4.0
+===========
+
+Version 4.0.0
+-------------
 
 This version adds the following features, outlined below. Please note that
 pVACtools 4.0 is not backwards-compatible and certain changes will break old
@@ -65,8 +68,8 @@ _____________
 - A new parameter ``--aggregate-inclusion-binding-threshold`` controls which
   epitope candidates are included in the aggregate report.
 
-New in Version 4.0.1
---------------------
+Version 4.0.1
+-------------
 
 This is a bugfix release. It fixes the following problem(s):
 
@@ -76,8 +79,8 @@ This is a bugfix release. It fixes the following problem(s):
 - Correctly set NA columns in pVACview export dataframe.
 - Handle Arriba files with empty peptide_sequence fields.
 
-New in Version 4.0.2
---------------------
+Version 4.0.2
+-------------
 
 This is a bugfix release. It fixes the following problem(s):
 
@@ -99,24 +102,24 @@ This is a bugfix release. It fixes the following problem(s):
   epitopes not being present in the "master" fasta file. This update brings
   both file creation steps in sync.
 
-New in Version 4.0.3
---------------------
+Version 4.0.3
+-------------
 
 This is a bugfix release. It fixes the following problem(s):
 
 - The fixes in issue in the reference proteome similarity step in pVACseq
   where running with non-human data would cause an error.
 
-New in Version 4.0.4
---------------------
+Version 4.0.4
+-------------
 
 This is a bugfix release. It fixes the following problem(s):
 
 - This release makes various fixes to allow pVACtools to run with non-human
   data.
 
-New in Version 4.0.5
---------------------
+Version 4.0.5
+-------------
 
 This is a bugfix release. It fixes the following problem(s):
 
@@ -129,3 +132,12 @@ This is a bugfix release. It fixes the following problem(s):
   However, we suspect that this causes a substantial increase in memory usage
   resulting in the observed behavior. This release reverts the change from PR
   988.
+
+This is a bugfix release. It fixes the following problem(s):
+
+Version 4.0.6
+-------------
+
+- A bug in the aggregate report creation incorrectly evaluated the Transcript
+  Support Level and resulted in picking the wrong Best Transcript in some
+  cases.
diff --git a/pvactools/lib/aggregate_all_epitopes.py b/pvactools/lib/aggregate_all_epitopes.py
@@ -334,7 +334,7 @@ def get_best_binder(self, df):
         #subset protein_coding dataframe to only include entries with a TSL < maximum_transcript_support_level
         tsl_df = biotype_df[biotype_df['Transcript Support Level'] != 'NA']
         tsl_df = tsl_df[tsl_df['Transcript Support Level'] != 'Not Supported']
-        tsl_df = tsl_df[tsl_df['Transcript Support Level'] < self.maximum_transcript_support_level]
+        tsl_df = tsl_df[tsl_df['Transcript Support Level'] <= self.maximum_transcript_support_level]
         #if this results in an empty dataframe, reset to previous dataframe
         if tsl_df.shape[0] == 0:
             tsl_df = biotype_df

diff --git a/setup.py b/setup.py
@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.0.5",
+    version="4.0.6",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",