From 3e71c2bc3eb9f8c3e91c41fccdfb3384211bdf14 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Tue, 22 Dec 2015 18:11:19 -0500
Subject: [PATCH] fixed incorrect assumptions about dict layout in synthesize
script
---
experiments/synthesize-augmented-dataset.py | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/experiments/synthesize-augmented-dataset.py b/experiments/synthesize-augmented-dataset.py
index 4d8ebc08..c332529c 100644
--- a/experiments/synthesize-augmented-dataset.py
+++ b/experiments/synthesize-augmented-dataset.py
@@ -85,9 +85,13 @@ if __name__ == "__main__":
print("Created reverse lookup dictionary for %d peptides" % len(reverse_lookup))
if args.allele_similarity_csv:
- sims_dict = load_sims_dict(args.allele_similarity_csv)
- print("Loaded similarities between %d allele pairs (%d unique)" % (
- len(sims_dict), len(set(a for (a, _) in sims_dict.keys()))))
+ sims_dict = load_sims_dict(
+ args.allele_similarity_csv,
+ allele_pair_keys=False)
+ allele_names = list(sims_dict.keys())
+ print("Loaded similarities between %d alleles from %s" % (
+ len(allele_names),
+ args.allele_similarity_csv))
else:
sims_dict, _, _ = \
compute_allele_similarities(
@@ -98,7 +102,8 @@ if __name__ == "__main__":
peptide_to_affinities=reverse_lookup,
pairwise_allele_similarities=sims_dict,
smoothing=args.smoothing_coef,
- exponent=args.similarity_exponent)
+ exponent=args.similarity_exponent,
+ allele_pair_keys=False)
synthetic_data_dict = OrderedDict([
("mhc", []),
--
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