From b8e4f2ef3082bf7fe73de340ba5a7e8147e71f83 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Wed, 1 Jul 2015 10:47:47 -0400
Subject: [PATCH] support more lengths
---
mhcflurry/mhc1_binding_predictor.py | 27 +++++++------------
.../train-class1-allele-specific-models.py | 9 ++++++-
2 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/mhcflurry/mhc1_binding_predictor.py b/mhcflurry/mhc1_binding_predictor.py
index 58f54e92..d3e437e5 100644
--- a/mhcflurry/mhc1_binding_predictor.py
+++ b/mhcflurry/mhc1_binding_predictor.py
@@ -98,7 +98,13 @@ class Mhc1BindingPredictor(object):
Difference from the paper: instead of taking the geometric mean,
we're taking the median of log-transformed IC50 values
"""
- if length == 8:
+ assert len(peptides) > 0
+ if length < 8 or length > 15:
+ raise ValueError("Invalid peptide length: %d (%s)" % (
+ length, peptides[0]))
+ elif length == 9:
+ return peptides
+ elif length == 8:
# extend each peptide by inserting every possible amino acid
# between base-1 positions 4-8
return [
@@ -107,27 +113,14 @@ class Mhc1BindingPredictor(object):
for i in xrange(3, 8)
for extra_amino_acid in amino_acid_letters
]
- if length == 9:
- return peptides
- elif length == 10:
+ else:
# drop interior residues between base-1 positions 4-9
+ n_skip = length - 9
return [
- peptide[:i] + peptide[i + 1:]
+ peptide[:i] + peptide[i + n_skip:]
for peptide in peptides
for i in range(3, 9)
]
- elif length == 11:
- # drop pairs of amino acids from interior residues
- return [
- peptide[:i] + peptide[i + 2:]
- for peptide in peptides
- for i in range(3, 9)
- ]
- else:
- raise ValueError(
- "Only lengths 8-11 supported, can't predict %s (len=%d)" % (
- peptides[0],
- length))
def predict_peptides(self, peptides):
column_names = [
diff --git a/scripts/train-class1-allele-specific-models.py b/scripts/train-class1-allele-specific-models.py
index e42e8b2d..e422588c 100755
--- a/scripts/train-class1-allele-specific-models.py
+++ b/scripts/train-class1-allele-specific-models.py
@@ -24,6 +24,7 @@ import argparse
import numpy as np
+from mhcflurry.common import normalize_allele_name
from mhcflurry.feedforward import make_network
from mhcflurry.data_helpers import load_data
from mhcflurry.class1_allele_specific_hyperparameters import (
@@ -88,10 +89,14 @@ if __name__ == "__main__":
activation=ACTIVATION,
init=INITIALIZATION_METHOD,
dropout_probability=DROPOUT_PROBABILITY)
+ print("Model config: %s" % (model.get_config(),))
model.fit(X_all, Y_all, nb_epoch=N_PRETRAIN_EPOCHS)
old_weights = model.get_weights()
for allele_name, allele_data in allele_groups.items():
- allele_name = allele_name.replace("/", "_").replace("*", "").replace(":", "")
+ allele_name = normalize_allele_name(allele_name)
+ if allele_name.isdigit():
+ print("Skipping allele %s" % (allele_name,))
+ continue
n_allele = len(allele_data.Y)
print("%s: total count = %d" % (allele_name, n_allele))
filename = allele_name + ".hdf"
@@ -101,10 +106,12 @@ if __name__ == "__main__":
continue
if n_allele < 10:
print("-- too few data points, skipping")
+ continue
model.set_weights(old_weights)
model.fit(
allele_data.X,
allele_data.Y,
nb_epoch=N_EPOCHS,
show_accuracy=True)
+ print("Saving model for %s to %s" % (allele_name, path))
model.save_weights(path)
--
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