Getting rid of sys.maxint (doesn't exist in Python3), just picking a …

…too-large number.
openvax · Sep 13, 2017 · c6d16b8 · c6d16b8
1 parent 9e050a9
commit c6d16b8
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git a/test/test_mutant_protein_sequence.py b/test/test_mutant_protein_sequence.py
@@ -15,7 +15,7 @@
 from __future__ import absolute_import, print_function, division
 from operator import attrgetter
 
-from nose.tools import eq_
+from nose.tools import eq_, assert_almost_equal
 from vaxrank.core_logic import ranked_vaccine_peptides
 from mhctools import RandomBindingPredictor
 from isovar.cli.variant_sequences import make_variant_sequences_arg_parser
@@ -132,4 +132,4 @@ def test_keep_top_k_epitopes():
         # propagated as expected
         mutant_epitope_score = sum(
             p.logistic_epitope_score() for p in vaccine_peptide.mutant_epitope_predictions)
-        eq_(mutant_epitope_score, vaccine_peptide.mutant_epitope_score)
+        assert_almost_equal(mutant_epitope_score, vaccine_peptide.mutant_epitope_score)
diff --git a/vaxrank/core_logic.py b/vaxrank/core_logic.py
@@ -14,7 +14,6 @@
 
 from __future__ import absolute_import, print_function, division
 import logging
-import sys
 
 from numpy import isclose
 
@@ -136,7 +135,7 @@ def generate_vaccine_peptides(
         min_alt_rna_reads,
         min_variant_sequence_coverage,
         variant_sequence_assembly,
-        num_mutant_epitopes_to_keep=sys.maxint,
+        num_mutant_epitopes_to_keep=10000,
         min_epitope_score=0):
     """
     Returns dictionary mapping each variant to list of VaccinePeptide objects.
@@ -179,7 +178,7 @@ def ranked_vaccine_peptides(
         min_alt_rna_reads,
         min_variant_sequence_coverage,
         variant_sequence_assembly,
-        num_mutant_epitopes_to_keep=sys.maxint,
+        num_mutant_epitopes_to_keep=10000,
         min_epitope_score=0):
     """
     Returns sorted list whose first element is a Variant and whose second

diff --git a/vaxrank/vaccine_peptide.py b/vaxrank/vaccine_peptide.py
@@ -17,7 +17,6 @@
 
 from collections import namedtuple
 from operator import attrgetter
-import sys
 
 import numpy as np
 
@@ -43,7 +42,7 @@ def __new__(
             cls,
             mutant_protein_fragment,
             epitope_predictions,
-            num_mutant_epitopes_to_keep=sys.maxint,
+            num_mutant_epitopes_to_keep=10000,
             min_epitope_score=0):
         # only keep the top k epitopes
         mutant_epitope_predictions = sorted([