From 2b38c362596b7f0cdb927bb3e76ceb011a3fe060 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Thu, 28 Apr 2016 18:56:50 -0400
Subject: [PATCH] added imputation module
---
mhcflurry/imputation.py | 155 +++++++++++++++++++++++++++++++++++++++
test/test_allele_data.py | 2 +-
2 files changed, 156 insertions(+), 1 deletion(-)
create mode 100644 mhcflurry/imputation.py
diff --git a/mhcflurry/imputation.py b/mhcflurry/imputation.py
new file mode 100644
index 00000000..f90ec29b
--- /dev/null
+++ b/mhcflurry/imputation.py
@@ -0,0 +1,155 @@
+# Copyright (c) 2015. Mount Sinai School of Medicine
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+)
+from collections import defaultdict
+import numpy as np
+
+def prune_dense_matrix_and_labels(
+ X,
+ peptide_list,
+ allele_list,
+ min_observations_per_peptide=1,
+ min_observations_per_allele=1):
+ """
+ Filter the dense matrix of pMHC binding affinities according to
+ the given minimum number of row/column observations.
+
+ Parameters
+ ----------
+ X : numpy.ndarray
+ Incomplete dense matrix of pMHC affinity with n_peptides rows and
+ n_alleles columns.
+
+ peptide_list : list of str
+ Expected to have n_peptides entries
+
+ allele_list : list of str
+ Expected to have n_alleles entries
+
+ min_observations_per_peptide : int
+ Drop peptide rows with fewer than this number of observed values.
+
+ min_observations_per_allele : int
+ Drop allele columns with fewer than this number of observed values.
+ """
+ observed_mask = np.isfinite(X)
+ n_observed_per_peptide = observed_mask.sum(axis=1)
+ too_few_peptide_observations = (
+ n_observed_per_peptide < min_observations_per_peptide)
+ if too_few_peptide_observations.any():
+ drop_peptide_indices = np.where(too_few_peptide_observations)[0]
+ keep_peptide_indices = np.where(~too_few_peptide_observations)[0]
+ print("Dropping %d peptides with <%d observations" % (
+ len(drop_peptide_indices),
+ min_observations_per_peptide))
+ X = X[keep_peptide_indices]
+ observed_mask = observed_mask[keep_peptide_indices]
+ peptide_list = [peptide_list[i] for i in keep_peptide_indices]
+
+ n_observed_per_allele = observed_mask.sum(axis=0)
+ too_few_allele_observations = (
+ n_observed_per_allele < min_observations_per_peptide)
+ if too_few_peptide_observations.any():
+ drop_allele_indices = np.where(too_few_allele_observations)[0]
+ keep_allele_indices = np.where(~too_few_allele_observations)[0]
+ print("Dropping %d alleles with <%d observations: %s" % (
+ len(drop_allele_indices),
+ min_observations_per_allele,
+ [allele_list[i] for i in drop_allele_indices]))
+ X = X[:, keep_allele_indices]
+ observed_mask = observed_mask[:, keep_allele_indices]
+ allele_list = [allele_list[i] for i in keep_allele_indices]
+ return X, peptide_list, allele_list
+
+def create_incompelte_dense_pMHC_matrix(
+ allele_data_dict,
+ min_observations_per_peptide=1,
+ min_observations_per_allele=1):
+ """
+ Given a dictionary mapping each allele name onto an AlleleData object,
+ returns a tuple with a dense matrix of affinities, a list of peptide labels
+ for each row and a list of allele labels for each column.
+
+ Parameters
+ ----------
+ allele_data_dict : dict
+ Dictionary mapping allele names to AlleleData objects
+
+ imputer : object
+ Expected to have a method imputer.complete(X) which takes an array
+ with missing entries marked by NaN and returns a completed array.
+
+ min_observations_per_peptide : int
+ Drop peptide rows with fewer than this number of observed values.
+
+ min_observations_per_allele : int
+ Drop allele columns with fewer than this number of observed values.
+ """
+ peptide_to_allele_to_affinity_dict = defaultdict(dict)
+ for (allele_name, allele_data) in allele_data_dict.items():
+ for peptide, affinity in zip(
+ allele_data.original_peptides,
+ allele_data.Y):
+ if allele_name not in peptide_to_allele_to_affinity_dict[peptide]:
+ peptide_to_allele_to_affinity_dict[peptide][allele_name] = affinity
+
+ n_binding_values = sum(
+ len(allele_dict)
+ for allele_dict in
+ allele_to_peptide_to_affinity.values()
+ )
+ print("Collected %d binding values for %d alleles" % (
+ n_binding_values,
+ len(peptide_to_allele_to_affinity_dict)))
+ X, peptide_list, allele_list = \
+ dense_matrix_from_nested_dictionary(peptide_to_allele_to_affinity)
+ return prune_data(
+ X,
+ peptide_list,
+ allele_list,
+ min_observations_per_peptide=min_observations_per_peptide,
+ min_observations_per_allele=min_observations_per_allele)
+
+
+def create_imputed_dataset(
+ allele_data_dict,
+ imputer,
+ min_observations_per_peptide=1,
+ min_observations_per_allele=1):
+ """
+ Parameters
+ ----------
+ allele_data_dict : dict
+ Dictionary mapping allele names to AlleleData objects
+
+ imputer : object
+ Expected to have a method imputer.complete(X) which takes an array
+ with missing entries marked by NaN and returns a completed array.
+
+ min_observations_per_peptide : int
+ Drop peptide rows with fewer than this number of observed values.
+
+ min_observations_per_allele : int
+ Drop allele columns with fewer than this number of observed values.
+ """
+ X_incomplete, peptide_list, allele_list = create_incompelte_dense_pMHC_matrix(
+ allele_data_dict=allele_data_dict,
+ min_observations_per_peptide=min_observations_per_peptide,
+ min_observations_per_allele=min_observations_per_allele)
+ X_complete = impute.complete(X_incomplete)
diff --git a/test/test_allele_data.py b/test/test_allele_data.py
index 8048cfe2..ae03863d 100644
--- a/test/test_allele_data.py
+++ b/test/test_allele_data.py
@@ -16,4 +16,4 @@ def test_create_allele_data_from_peptide_to_ic50_dict():
"C" * 9,
])
peptides = set(allele_data.peptides)
- eq_(expected_peptides, peptides)
\ No newline at end of file
+ eq_(expected_peptides, peptides)
--
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