Propagating --do-not-raise-on-error as a CLI arg for IEDB constructor…

…s. Also some logging updates

mhctools/__init__.py

@@ -22,7 +22,7 @@
 from .random_predictor import RandomBindingPredictor
 from .unsupported_allele import UnsupportedAllele
 
-__version__ = "1.8.1"
+__version__ = "1.8.2"
 
 __all__ = [
     "BindingPrediction",

mhctools/cli/args.py

@@ -128,6 +128,11 @@ def add_mhc_args(arg_parser):
         default="",
         help="Comma or space separated list of allele (default HLA-A*02:01)")
 
+    mhc_options_arg_group.add_argument(
+        "--do-not-raise-on-error",
+        action="store_true", default=False,
+        help="If this arg is present, will not crash on error. Only applies to IEDB predictors")
+
     return mhc_options_arg_group
 
 
@@ -180,4 +185,7 @@ def mhc_binding_predictor_from_args(args):
     if args.mhc_predictor_path:
         kwargs["program_name"] = args.mhc_predictor_path
 
+    if args.do_not_raise_on_error:
+        kwargs["raise_on_error"] = False
+
     return mhc_class(**kwargs)

mhctools/cli/script.py

@@ -22,8 +22,9 @@
 from pyensembl.fasta import parse_fasta_dictionary
 
 from .args import make_mhc_arg_parser, mhc_binding_predictor_from_args
+from mhctools.logging import get_logger
+
 
-logging.config.fileConfig(pkg_resources.resource_filename(__name__, 'logging.conf'))
 logger = logging.getLogger(__name__)
 
 

mhctools/iedb.py

@@ -13,7 +13,6 @@
 # limitations under the License.
 
 from __future__ import print_function, division, absolute_import
-import logging
 import io
 
 # pylint: disable=import-error
@@ -31,6 +30,7 @@
 from .common import seq_to_str, check_sequence_dictionary
 from .binding_prediction import BindingPrediction
 from .binding_prediction_collection import BindingPredictionCollection
+from .logging import get_logger
 
 """
 A note about prediction methods, copied from the IEDB website:
@@ -50,7 +50,7 @@
 """
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 VALID_CLASS_I_METHODS = [
@@ -195,7 +195,7 @@ def predict_peptides(self, peptides):
                 binding_predictions,
                 peptides=peptides,
                 alleles=self.alleles)
-        except ValueError as e:
+        except Exception as e:
             if self.raise_on_error:
                 raise e
             else:
@@ -251,7 +251,7 @@ def predict_subsequences(self, sequence_dict, peptide_lengths=None):
                                 affinity=row['ic50'],
                                 percentile_rank=row['rank'],
                                 prediction_method_name="iedb-" + self.prediction_method))
-                except ValueError as e:
+                except Exception as e:
                     if self.raise_on_error:
                         raise e
                     else:
@@ -262,7 +262,7 @@ def predict_subsequences(self, sequence_dict, peptide_lengths=None):
                 binding_predictions,
                 alleles=normalized_alleles,
                 peptides=expected_peptides)
-        except ValueError as e:
+        except Exception as e:
             if self.raise_on_error:
                 raise e
             else:

mhctools/logging.py

@@ -0,0 +1,10 @@
+from __future__ import print_function, division, absolute_import
+
+import logging
+import logging.config
+import pkg_resources
+
+
+def get_logger(name):
+    logging.config.fileConfig(pkg_resources.resource_filename('mhctools', 'logging.conf'))
+    return logging.getLogger(name)

setup.py

@@ -42,12 +42,12 @@
         name='mhctools',
         version=version,
         description="Python interface to running command-line and web-based MHC binding predictors",
-        author="Alex Rubinsteyn",
-        author_email="alex.rubinsteyn@mssm.edu",
+        author="Alex Rubinsteyn, Julia Kodysh, Tim O'Donnell",
+        author_email="alex@openvax.org, julia@openvax.org, tim@openvax.org",
         url="https://github.com/openvax/mhctools",
         license="http://www.apache.org/licenses/LICENSE-2.0.html",
         classifiers=[
-            'Development Status :: 3 - Alpha',
+            'Development Status :: 4 - Beta',
             'Environment :: Console',
             'Operating System :: OS Independent',
             'Intended Audience :: Science/Research',
@@ -68,7 +68,9 @@
         long_description=readme_markdown,
         long_description_content_type="text/markdown",
         packages=['mhctools', 'mhctools.cli'],
-        package_data={'mhctools.cli': ['logging.conf']},
+        package_data={
+            'mhctools.cli': ['logging.conf'],
+            'mhctools': ['logging.conf']},
         entry_points={
             'console_scripts': [
                 'mhctools = mhctools.cli.script:main'