From 873a60a5f83973165680f8577a5c76ee3a260a0a Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 30 Nov 2017 12:55:23 -0500
Subject: [PATCH] More speed efficient variable-length peptide encoding
---
mhcflurry/amino_acid.py | 10 +--
mhcflurry/encodable_sequences.py | 105 ++++++++++++++++---------------
2 files changed, 59 insertions(+), 56 deletions(-)
diff --git a/mhcflurry/amino_acid.py b/mhcflurry/amino_acid.py
index c412dcad..c9057d9a 100644
--- a/mhcflurry/amino_acid.py
+++ b/mhcflurry/amino_acid.py
@@ -135,7 +135,7 @@ def index_encoding(sequences, letter_to_index_dict):
return result.values
-def fixed_vectors_encoding(sequences, letter_to_vector_df):
+def fixed_vectors_encoding(index_encoded_sequences, letter_to_vector_df):
"""
Given a sequence of n strings all of length k, and a dataframe mapping each
character to an arbitrary vector, return a n * k * m array where
@@ -152,10 +152,10 @@ def fixed_vectors_encoding(sequences, letter_to_vector_df):
numpy.array of integers with shape (n, k, m)
"""
target_shape = (
- len(sequences),
- len(sequences[0]),
+ len(index_encoded_sequences),
+ len(index_encoded_sequences[0]),
letter_to_vector_df.shape[0])
- result = letter_to_vector_df.loc[
- (letter for seq in sequences for letter in seq)
+ result = letter_to_vector_df.iloc[
+ index_encoded_sequences.flat
].values.reshape(target_shape)
return result
diff --git a/mhcflurry/encodable_sequences.py b/mhcflurry/encodable_sequences.py
index ca71ba68..b98fb862 100644
--- a/mhcflurry/encodable_sequences.py
+++ b/mhcflurry/encodable_sequences.py
@@ -86,16 +86,13 @@ class EncodableSequences(object):
max_length)
if cache_key not in self.encoding_cache:
- fixed_length_sequences = [
- self.sequence_to_fixed_length_string(
- sequence,
+ fixed_length_sequences = (
+ self.sequences_to_fixed_length_index_encoded_array(
+ self.sequences,
left_edge=left_edge,
right_edge=right_edge,
- max_length=max_length)
- for sequence in self.sequences
- ]
- self.encoding_cache[cache_key] = amino_acid.index_encoding(
- fixed_length_sequences, amino_acid.AMINO_ACID_INDEX)
+ max_length=max_length))
+ self.encoding_cache[cache_key] = fixed_length_sequences
return self.encoding_cache[cache_key]
def variable_length_to_fixed_length_vector_encoding(
@@ -130,14 +127,12 @@ class EncodableSequences(object):
right_edge,
max_length)
if cache_key not in self.encoding_cache:
- fixed_length_sequences = [
- self.sequence_to_fixed_length_string(
- sequence,
+ fixed_length_sequences = (
+ self.sequences_to_fixed_length_index_encoded_array(
+ self.sequences,
left_edge=left_edge,
right_edge=right_edge,
- max_length=max_length)
- for sequence in self.sequences
- ]
+ max_length=max_length))
result = amino_acid.fixed_vectors_encoding(
fixed_length_sequences,
amino_acid.ENCODING_DFS[vector_encoding_name])
@@ -145,25 +140,26 @@ class EncodableSequences(object):
self.encoding_cache[cache_key] = result
return self.encoding_cache[cache_key]
-
@classmethod
- def sequence_to_fixed_length_string(
- klass, sequence, left_edge=4, right_edge=4, max_length=15):
+ def sequences_to_fixed_length_index_encoded_array(
+ klass, sequences, left_edge=4, right_edge=4, max_length=15):
"""
- Transform a string of length at least left_edge + right_edge and at
- most max_length into a string of length max_length using a scheme
- designed to preserve the anchor positions of class I peptides.
-
+ Transform a sequence of strings, where each string is of length at least
+ left_edge + right_edge and at most max_length into strings of length
+ max_length using a scheme designed to preserve the anchor positions of
+ class I peptides.
+
The first left_edge characters in the input always map to the first
left_edge characters in the output. Similarly for the last right_edge
characters. The middle characters are filled in based on the length,
with the X character filling in the blanks.
-
+
For example, using defaults:
-
+
AAAACDDDD -> AAAAXXXCXXXDDDD
-
-
+
+ The strings are also converted to int categorical amino acid indices.
+
Parameters
----------
sequence : string
@@ -173,30 +169,37 @@ class EncodableSequences(object):
Returns
-------
- string of length max_length
-
+ numpy array of shape (len(sequences), max_length, 21) and dtype int
"""
- if len(sequence) < left_edge + right_edge:
- raise ValueError(
- "Sequence '%s' (length %d) unsupported: length must be at "
- "least %d" % (sequence, len(sequence), left_edge + right_edge))
- if len(sequence) > max_length:
- raise ValueError(
- "Sequence '%s' (length %d) unsupported: length must be at "
- "most %d" % (sequence, len(sequence), max_length))
-
- middle_length = max_length - left_edge - right_edge
-
- num_null = max_length - len(sequence)
- num_null_left = int(math.ceil(num_null / 2))
- num_null_right = int(math.floor(num_null / 2))
- num_not_null_middle = middle_length - num_null
- string_encoding = "".join([
- sequence[:left_edge],
- klass.unknown_character * num_null_left,
- sequence[left_edge:left_edge + num_not_null_middle],
- klass.unknown_character * num_null_right,
- sequence[-right_edge:],
- ])
- assert len(string_encoding) == max_length
- return string_encoding
+ result = numpy.ones(shape=(len(sequences), max_length), dtype=int) * -1
+ fill_value = amino_acid.AMINO_ACID_INDEX['X']
+ for (i, sequence) in enumerate(sequences):
+ sequence_indexes = [
+ amino_acid.AMINO_ACID_INDEX[char] for char in sequence
+ ]
+
+ if len(sequence) < left_edge + right_edge:
+ raise ValueError(
+ "Sequence '%s' (length %d) unsupported: length must be at "
+ "least %d" % (
+ sequence, len(sequence), left_edge + right_edge))
+ if len(sequence) > max_length:
+ raise ValueError(
+ "Sequence '%s' (length %d) unsupported: length must be at "
+ "most %d" % (sequence, len(sequence), max_length))
+
+ middle_length = max_length - left_edge - right_edge
+ num_null = max_length - len(sequence)
+ num_null_left = int(math.ceil(num_null / 2))
+ num_null_right = int(math.floor(num_null / 2))
+ num_not_null_middle = middle_length - num_null
+
+ result[i] = numpy.concatenate([
+ sequence_indexes[:left_edge],
+ numpy.ones(num_null_left) * fill_value,
+ sequence_indexes[left_edge:left_edge + num_not_null_middle],
+ numpy.ones(num_null_right) * fill_value,
+ sequence_indexes[-right_edge:],
+ ])
+ assert len(result[i]) == max_length
+ return result
--
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