From 36d65c3997ce1104c7967233ce7ed24e822d7d82 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 4 Feb 2020 15:34:38 -0500
Subject: [PATCH] fix
---
mhcflurry/class1_affinity_predictor.py | 4 +-
test/test_batch_generator.py | 100 ------------------
test/test_class1_processing_neural_network.py | 4 -
3 files changed, 3 insertions(+), 105 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 2b08a6ec..b6f2d903 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -419,7 +419,9 @@ class Class1AffinityPredictor(object):
series = transform.to_series()
if percent_ranks_df is None:
percent_ranks_df = pandas.DataFrame(index=series.index)
- assert_equal(series.index.values, percent_ranks_df.index.values)
+ numpy.testing.assert_array_almost_equal(
+ series.index.values,
+ percent_ranks_df.index.values)
percent_ranks_df[allele] = series
percent_ranks_path = join(models_dir, "percent_ranks.csv")
percent_ranks_df.to_csv(
diff --git a/test/test_batch_generator.py b/test/test_batch_generator.py
index 3cc6c11c..02779542 100644
--- a/test/test_batch_generator.py
+++ b/test/test_batch_generator.py
@@ -11,7 +11,6 @@ import pstats
import pandas
import numpy
-from mhcflurry.allele_encoding import MultipleAlleleEncoding
from mhcflurry.downloads import get_path
from mhcflurry.batch_generator import (
MultiallelicMassSpecBatchGenerator)
@@ -119,102 +118,3 @@ def test_basic():
experiment_allele_colocations[('exp2', 'HLA-A*03:01')],
experiment_allele_colocations[('exp2', 'HLA-A*02:01')])
-
-def test_large(sample_rate=1.0):
- multi_train_df = pandas.read_csv(
- data_path("multiallelic_ms.benchmark1.csv.bz2"))
- multi_train_df["label"] = multi_train_df.hit
- multi_train_df["is_affinity"] = False
-
- sample_table = multi_train_df.loc[
- multi_train_df.label == True
- ].drop_duplicates("sample_id").set_index("sample_id").loc[
- multi_train_df.sample_id.unique()
- ]
- grouped = multi_train_df.groupby("sample_id").nunique()
- for col in sample_table.columns:
- if (grouped[col] > 1).any():
- del sample_table[col]
- sample_table["alleles"] = sample_table.hla.str.split()
-
- pan_train_df = pandas.read_csv(
- get_path(
- "models_class1_pan", "models.combined/train_data.csv.bz2"))
- pan_sub_train_df = pan_train_df
- pan_sub_train_df["label"] = pan_sub_train_df["measurement_value"]
- del pan_sub_train_df["measurement_value"]
- pan_sub_train_df["is_affinity"] = True
-
- pan_sub_train_df = pan_sub_train_df.sample(frac=sample_rate)
- multi_train_df = multi_train_df.sample(frac=sample_rate)
-
- pan_predictor = Class1AffinityPredictor.load(
- get_path("models_class1_pan", "models.combined"),
- optimization_level=0,
- max_models=1)
-
- allele_encoding = MultipleAlleleEncoding(
- experiment_names=multi_train_df.sample_id.values,
- experiment_to_allele_list=sample_table.alleles.to_dict(),
- max_alleles_per_experiment=sample_table.alleles.str.len().max(),
- allele_to_sequence=pan_predictor.allele_to_sequence,
- )
- allele_encoding.append_alleles(pan_sub_train_df.allele.values)
- allele_encoding = allele_encoding.compact()
-
- combined_train_df = pandas.concat(
- [multi_train_df, pan_sub_train_df], ignore_index=True, sort=True)
-
- print("Total size", combined_train_df)
-
- planner = MultiallelicMassSpecBatchGenerator(
- hyperparameters=dict(
- batch_generator_validation_split=0.2,
- batch_generator_batch_size=128,
- batch_generator_affinity_fraction=0.5))
-
- s = time.time()
- profiler = cProfile.Profile()
- profiler.enable()
- planner.plan(
- affinities_mask=combined_train_df.is_affinity.values,
- experiment_names=combined_train_df.sample_id.values,
- alleles_matrix=allele_encoding.alleles,
- is_binder=numpy.where(
- combined_train_df.is_affinity.values,
- combined_train_df.label.values,
- to_ic50(combined_train_df.label.values)) < 1000.0)
- profiler.disable()
- stats = pstats.Stats(profiler)
- stats.sort_stats("cumtime").reverse_order().print_stats()
- print(planner.summary())
- print("Planning took [sec]: ", time.time() - s)
-
- (train_iter, test_iter) = planner.get_train_and_test_generators(
- x_dict={
- "idx": numpy.arange(len(combined_train_df)),
- },
- y_list=[])
-
- train_batch_sizes = []
- indices_total = numpy.zeros(len(combined_train_df))
- for (kind, it) in [("train", train_iter), ("test", test_iter)]:
- for (i, (x_item, y_item)) in enumerate(it):
- idx = x_item["idx"]
- indices_total[idx] += 1
- batch_df = combined_train_df.iloc[idx]
- if not batch_df.is_affinity.all():
- # Test each batch has at most one multiallelic ms experiment.
- assert_equal(
- batch_df.loc[~batch_df.is_affinity].sample_id.nunique(), 1)
- if kind == "train":
- train_batch_sizes.append(len(batch_df))
-
- # At most one short batch.
- assert_less(sum(b != 128 for b in train_batch_sizes), 2)
- assert_greater(
- sum(b == 128 for b in train_batch_sizes), len(train_batch_sizes) - 2)
-
- # Each point used exactly once.
- assert_equal(
- indices_total, numpy.ones(len(combined_train_df)))
diff --git a/test/test_class1_processing_neural_network.py b/test/test_class1_processing_neural_network.py
index a0e100c4..0a1368bd 100644
--- a/test/test_class1_processing_neural_network.py
+++ b/test/test_class1_processing_neural_network.py
@@ -131,10 +131,6 @@ def test_neural_network_input():
results['peptide_length'], df.peptide.str.len().values)
-def test_big():
- train_basic_network(num=100000)
-
-
def test_small():
train_basic_network(num=10000)
--
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