Merge pull request #93 from griffithlab/warning

Better warning messages if alleles and prediction algorithms are not compatible

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.1'
+release = '1.0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -38,12 +38,25 @@ New in version |release|
 
 This is a hotfix release. It fixes the following issues:
 
-- Additional data, like example data and VEP plugins were not included in the
-  package correctly so the commands to download these files would fail. This
-  has been corrected.
-- Class II predictions would fail if the protein sequences used for binding
-  predictions in IEDB were shorter than 15 peptide sequences. This has been
-  fixed.
+- The epitope length used for generating the peptide fasta when running with
+  multiple epitope lengths was incorrect. This would potentially result in including
+  fasta sequences that were shorter than the largest epitope length which
+  would cause an error during calls to IEDB.
+- pVACseq would fail with a nondescript error message if the input VCF was not
+  annotated with VEP before running. A more descriptive error message has been
+  added.
+- IEDB changed the format of class II IEDB alleles which would cause an error
+  when running with those alleles. pVACtools will now handle transposing the
+  affected alleles into the new format.
+- The standalone binding filters had a few bugs that would result in syntax
+  errors during runtime.
+- The indexes created for each fusion entry with pVACfuse had the potential to
+  not be unique which would result in parsing errors downstream.
+- pVACseq had the potential to use the incorrect VEP allele for positions with
+  multiple alternate alleles which would result in the incorrect CSQ entry
+  getting used for some of those alternate alleles.
+- pVACseq would throw an error if the chosen peptide sequence length exceeds
+  the wildtype protein sequence length of a transcript.
 
 Coming soon
 -----------

setup.py

@@ -45,7 +45,7 @@
 
 setup(
     name="pvactools",
-    version="1.0.1",
+    version="1.0.2",
     packages=["tools", "tools.pvacfuse", "tools.pvacvector", "tools.pvacseq", "lib", "utils.pvacapi", "utils.pvacapi.controllers"],
     entry_points={
         "console_scripts":[

tools/pvacseq/run.py

@@ -124,6 +124,10 @@ def main(args_input = sys.argv[1:]):
         class_i_arguments['netmhc_stab']             = args.netmhc_stab
         pipeline = MHCIPipeline(**class_i_arguments)
         pipeline.execute()
+    elif len(class_i_prediction_algorithms) == 0:
+        print("No MHC class I prediction algorithms chosen. Skipping MHC class I predictions.")
+    elif len(class_i_alleles) == 0:
+        print("No MHC class I alleles chosen. Skipping MHC class I predictions.")
 
     if len(class_ii_prediction_algorithms) > 0 and len(class_ii_alleles) > 0:
         if args.iedb_install_directory:
@@ -146,6 +150,10 @@ def main(args_input = sys.argv[1:]):
         class_ii_arguments['netmhc_stab']           = False
         pipeline = MHCIIPipeline(**class_ii_arguments)
         pipeline.execute()
+    elif len(class_ii_prediction_algorithms) == 0:
+        print("No MHC class II prediction algorithms chosen. Skipping MHC class II predictions.")
+    elif len(class_ii_alleles) == 0:
+        print("No MHC class II alleles chosen. Skipping MHC class II predictions.")
 
 if __name__ == '__main__':
     main()