From 6f6070b23a0e152a947f6b2909d80f87214bd9db Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 10 Dec 2017 20:01:07 -0500
Subject: [PATCH] formatting changes
---
mhcflurry/encodable_sequences.py | 21 ++++++++++++---------
1 file changed, 12 insertions(+), 9 deletions(-)
diff --git a/mhcflurry/encodable_sequences.py b/mhcflurry/encodable_sequences.py
index d2a06498..e7373758 100644
--- a/mhcflurry/encodable_sequences.py
+++ b/mhcflurry/encodable_sequences.py
@@ -202,30 +202,33 @@ class EncodableSequences(object):
# Array of shape (num peptides, length) giving fixed-length amino
# acid encoding each peptide of the current length.
- fixed_length_indices = numpy.stack(
+ fixed_length_sequences = numpy.stack(
sub_df.peptide.map(
- lambda s: numpy.array(
- [amino_acid.AMINO_ACID_INDEX[char] for char in
- s])).values)
+ lambda s: numpy.array([
+ amino_acid.AMINO_ACID_INDEX[char] for char in s
+ ])).values)
num_null = max_length - length
num_null_left = int(math.ceil(num_null / 2))
- num_not_null_middle = middle_length - num_null
+ num_middle_filled = middle_length - num_null
+ middle_start = left_edge + num_null_left
# Set left edge
- result[sub_df.index, :left_edge] = fixed_length_indices[
+ result[sub_df.index, :left_edge] = fixed_length_sequences[
:, :left_edge
]
# Set middle.
result[
sub_df.index,
- left_edge + num_null_left : left_edge + num_null_left + num_not_null_middle
- ] = fixed_length_indices[:, left_edge:left_edge + num_not_null_middle]
+ middle_start : middle_start + num_middle_filled
+ ] = fixed_length_sequences[
+ :, left_edge : left_edge + num_middle_filled
+ ]
# Set right edge.
result[
sub_df.index,
-right_edge:
- ] = fixed_length_indices[:, -right_edge:]
+ ] = fixed_length_sequences[:, -right_edge:]
return result
--
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