From e4c21bcba014600c072bb1bc9e0d6313fb205d2c Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 24 Nov 2017 18:01:36 -0500
Subject: [PATCH] Add throw argument to percentile_ranks
---
.../class1_affinity_predictor.py | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
index d0e84024..c3b841da 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
@@ -525,7 +525,7 @@ class Class1AffinityPredictor(object):
transform.fit(predictions, bins=bins)
self.allele_to_percent_rank_transform[allele] = transform
- def percentile_ranks(self, affinities, allele=None, alleles=None):
+ def percentile_ranks(self, affinities, allele=None, alleles=None, throw=True):
"""
Return percentile ranks for the given ic50 affinities and alleles.
@@ -538,6 +538,10 @@ class Class1AffinityPredictor(object):
nM affinities
allele : string
alleles : sequence of string
+ throw : boolean
+ If True, a ValueError will be raised in the case of unsupported
+ alleles. If False, a warning will be logged and NaN will be returned
+ for those percentile ranks.
Returns
-------
@@ -548,8 +552,13 @@ class Class1AffinityPredictor(object):
transform = self.allele_to_percent_rank_transform[allele]
return transform.transform(affinities)
except KeyError:
- raise ValueError(
- "Allele %s has no percentile rank information" % allele)
+ msg = "Allele %s has no percentile rank information" % allele
+ if throw:
+ raise ValueError(msg)
+ else:
+ warnings.warn(msg)
+ # Return NaNs
+ return numpy.ones(len(affinities)) * numpy.nan
if alleles is None:
raise ValueError("Specify allele or alleles")
@@ -559,7 +568,7 @@ class Class1AffinityPredictor(object):
df["result"] = numpy.nan
for (allele, sub_df) in df.groupby("allele"):
df.loc[sub_df.index, "result"] = self.percentile_ranks(
- sub_df.affinity, allele=allele)
+ sub_df.affinity, allele=allele, throw=throw)
assert not df.result.isnull().any()
return df.result.values
@@ -752,7 +761,7 @@ class Class1AffinityPredictor(object):
if include_percentile_ranks:
if self.allele_to_percent_rank_transform:
result["prediction_percentile"] = self.percentile_ranks(
- df.prediction, alleles=df.allele.values)
+ df.prediction, alleles=df.allele.values, throw=throw)
else:
warnings.warn("No percentile rank information available.")
return result
--
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