From d7e3af613913b008d7a41a8b35aa9eaccb59ab3b Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 23 Feb 2018 12:12:50 -0500
Subject: [PATCH] Default to no extra decoys in mass spec model selection
---
.../select_allele_specific_models_command.py | 31 ++++++++++++-------
1 file changed, 19 insertions(+), 12 deletions(-)
diff --git a/mhcflurry/select_allele_specific_models_command.py b/mhcflurry/select_allele_specific_models_command.py
index f6cd6e85..01587d76 100644
--- a/mhcflurry/select_allele_specific_models_command.py
+++ b/mhcflurry/select_allele_specific_models_command.py
@@ -482,23 +482,30 @@ class MassSpecModelSelector(object):
self,
df,
predictor,
- decoys_per_length=5000,
+ decoys_per_length=0,
min_measurements=100,
multiply_score_by_data_size=True):
- (min_length, max_length) = predictor.supported_peptide_lengths
- decoys = []
- for length in range(min_length, max_length + 1):
- decoys.extend(
- random_peptides(decoys_per_length, length=length))
-
# Index is peptide, columns are alleles
- hit_matrix = df.groupby(["peptide", "allele"]).measurement_value.count().unstack().fillna(0).astype(bool)
+ hit_matrix = df.groupby(
+ ["peptide", "allele"]).measurement_value.count().unstack().fillna(
+ 0).astype(bool)
+
+ if decoys_per_length:
+ (min_length, max_length) = predictor.supported_peptide_lengths
+ decoys = []
+ for length in range(min_length, max_length + 1):
+ decoys.extend(
+ random_peptides(decoys_per_length, length=length))
+
+ decoy_matrix = pandas.DataFrame(
+ index=decoys, columns=hit_matrix.columns, dtype=bool)
+ decoy_matrix[:] = False
+ full_matrix = pandas.concat([hit_matrix, decoy_matrix])
+ else:
+ full_matrix = hit_matrix
- decoy_matrix = pandas.DataFrame(
- index=decoys, columns=hit_matrix.columns, dtype=bool)
- decoy_matrix[:] = False
- full_matrix = pandas.concat([hit_matrix, decoy_matrix]).sample(frac=1.0)
+ full_matrix = full_matrix.sample(frac=1.0)
self.df = full_matrix
self.predictor = predictor
--
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