From 764d8594b976103bd706bbf4abc958fdf47eccd1 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 16 Feb 2018 16:10:35 -0500
Subject: [PATCH] fix
---
mhcflurry/class1_affinity_predictor.py | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 2ad081f6..406baf79 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -827,11 +827,14 @@ class Class1AffinityPredictor(object):
if alleles is not None:
raise ValueError("Specify exactly one of allele or alleles")
df["allele"] = allele
- df["normalized_allele"] = mhcnames.normalize_allele_name(allele)
+ normalized_allele = mhcnames.normalize_allele_name(allele)
+ df["normalized_allele"] = normalized_allele
+ unique_alleles = [normalized_allele]
else:
df["allele"] = numpy.array(alleles)
df["normalized_allele"] = df.allele.map(
mhcnames.normalize_allele_name)
+ unique_alleles = df.normalized_allele.unique()
if len(df) == 0:
# No predictions.
@@ -854,8 +857,8 @@ class Class1AffinityPredictor(object):
# Only compute this if needed
all_peptide_lengths_supported = False
df["supported_peptide_length"] = (
- (df.sequence_length.len() >= min_peptide_length) &
- (df.sequence_length.len() <= max_peptide_length))
+ (df.sequence_length >= min_peptide_length) &
+ (df.sequence_length <= max_peptide_length))
if (~df.supported_peptide_length).any():
msg = (
"%d peptides have lengths outside of supported range [%d, %d]: "
@@ -899,9 +902,8 @@ class Class1AffinityPredictor(object):
allele_encoding=masked_allele_encoding)
if self.allele_to_allele_specific_models:
- query_alleles = df.normalized_allele.unique()
unsupported_alleles = [
- allele for allele in query_alleles
+ allele for allele in unique_alleles
if not self.allele_to_allele_specific_models.get(allele)
]
if unsupported_alleles:
@@ -914,9 +916,9 @@ class Class1AffinityPredictor(object):
if throw:
raise ValueError(msg)
- for allele in query_alleles:
+ for allele in unique_alleles:
models = self.allele_to_allele_specific_models.get(allele, [])
- if len(query_alleles) == 1 and all_peptide_lengths_supported:
+ if len(unique_alleles) == 1 and all_peptide_lengths_supported:
mask = None
else:
mask = (
--
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