From 024cb70eae4995e2238600d3358c035af26f50a0 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 19 Apr 2019 14:33:13 -0400
Subject: [PATCH] add support for left_pad_right_pad in encodable_sequences
---
mhcflurry/encodable_sequences.py | 37 +++++++++++++++++++++++++++++---
1 file changed, 34 insertions(+), 3 deletions(-)
diff --git a/mhcflurry/encodable_sequences.py b/mhcflurry/encodable_sequences.py
index 2560a8ef..8dff8e8f 100644
--- a/mhcflurry/encodable_sequences.py
+++ b/mhcflurry/encodable_sequences.py
@@ -51,7 +51,11 @@ class EncodableSequences(object):
return len(self.sequences)
def variable_length_to_fixed_length_categorical(
- self, left_edge=4, right_edge=4, max_length=15):
+ self,
+ alignment_method="pad_middle",
+ left_edge=4,
+ right_edge=4,
+ max_length=15):
"""
Encode variable-length sequences using a fixed-length encoding designed
for preserving the anchor positions of class I peptides.
@@ -80,6 +84,7 @@ class EncodableSequences(object):
fixed_length_sequences = (
self.sequences_to_fixed_length_index_encoded_array(
self.sequences,
+ alignment_method=alignment_method,
left_edge=left_edge,
right_edge=right_edge,
max_length=max_length))
@@ -87,7 +92,12 @@ class EncodableSequences(object):
return self.encoding_cache[cache_key]
def variable_length_to_fixed_length_vector_encoding(
- self, vector_encoding_name, left_edge=4, right_edge=4, max_length=15):
+ self,
+ vector_encoding_name,
+ alignment_method="pad_middle",
+ left_edge=4,
+ right_edge=4,
+ max_length=15):
"""
Encode variable-length sequences using a fixed-length encoding designed
for preserving the anchor positions of class I peptides.
@@ -120,6 +130,7 @@ class EncodableSequences(object):
fixed_length_sequences = (
self.sequences_to_fixed_length_index_encoded_array(
self.sequences,
+ alignment_method=alignment_method,
left_edge=left_edge,
right_edge=right_edge,
max_length=max_length))
@@ -227,7 +238,27 @@ class EncodableSequences(object):
-right_edge:
] = fixed_length_sequences[:, -right_edge:]
elif alignment_method == "left_pad_right_pad":
- raise NotImplementedError
+ # Result array is int32, filled with X (null amino acid) value.
+ result = numpy.full(fill_value=amino_acid.AMINO_ACID_INDEX['X'],
+ shape=(len(sequences), max_length * 2), dtype="int32")
+
+ df = pandas.DataFrame({"peptide": sequences})
+
+ # For efficiency we handle each supported peptide length using bulk
+ # array operations.
+ for (length, sub_df) in df.groupby(df.peptide.str.len()):
+ # Array of shape (num peptides, length) giving fixed-length amino
+ # acid encoding each peptide of the current length.
+ fixed_length_sequences = numpy.stack(sub_df.peptide.map(
+ lambda s: numpy.array(
+ [amino_acid.AMINO_ACID_INDEX[char] for char in
+ s])).values)
+
+ # Set left edge
+ result[sub_df.index, :length] = fixed_length_sequences
+
+ # Set right edge.
+ result[sub_df.index, -length:] = fixed_length_sequences
else:
raise NotImplementedError(
"Unsupported alignment method: %s" % alignment_method)
--
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