From 7a54300bf2347662a58808584b87dfb5c3fbbfc1 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 6 Sep 2019 15:27:33 -0400
Subject: [PATCH] truncate huge error message when missing an allele in the
pan-allele predictor
---
mhcflurry/class1_affinity_predictor.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 10ae6365..6068581a 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -1079,11 +1079,16 @@ class Class1AffinityPredictor(object):
if allele not in self.allele_to_sequence
]
if unsupported_alleles:
+ truncate_at = 100
+ allele_string = " ".join(
+ sorted(self.allele_to_sequence)[:truncate_at])
+ if len(self.allele_to_sequence) > truncate_at:
+ allele_string += " + %d more alleles" % (
+ len(self.allele_to_sequence) - truncate_at)
msg = (
"No sequences for allele(s): %s.\n"
"Supported alleles: %s" % (
- " ".join(unsupported_alleles),
- " ".join(sorted(self.allele_to_sequence))))
+ " ".join(unsupported_alleles), allele_string))
logging.warning(msg)
if throw:
raise ValueError(msg)
--
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