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Commit ff2bfc1c authored by Tim O'Donnell's avatar Tim O'Donnell
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fix

parent bcf82146
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"""
Tests for training and predicting using Class1 pan-allele models.
"""
import logging
logging.getLogger('tensorflow').disabled = True
logging.getLogger('matplotlib').disabled = True
from sklearn.metrics import roc_auc_score
import pandas
from numpy.testing import assert_, assert_equal
from mhcflurry import Class1AffinityPredictor,Class1NeuralNetwork
from mhcflurry import Class1AffinityPredictor, Class1NeuralNetwork
from mhcflurry.allele_encoding import AlleleEncoding
from mhcflurry.downloads import get_path
......@@ -63,7 +66,7 @@ ALLELE_TO_SEQUENCE = pandas.read_csv(
TRAIN_DF = pandas.read_csv(
get_path(
"data_curated", "curated_training_data.no_mass_spec.csv.bz2"))
"data_curated", "curated_training_data.affinity.csv.bz2"))
TRAIN_DF = TRAIN_DF.loc[TRAIN_DF.allele.isin(ALLELE_TO_SEQUENCE)]
TRAIN_DF = TRAIN_DF.loc[TRAIN_DF.peptide.str.len() >= 8]
......@@ -76,7 +79,7 @@ TRAIN_DF = TRAIN_DF.loc[
MS_HITS_DF = pandas.read_csv(
get_path(
"data_curated", "curated_training_data.with_mass_spec.csv.bz2"))
"data_curated", "curated_training_data.csv.bz2"))
MS_HITS_DF = MS_HITS_DF.loc[MS_HITS_DF.allele.isin(TRAIN_DF.allele.unique())]
MS_HITS_DF = MS_HITS_DF.loc[MS_HITS_DF.peptide.str.len() >= 8]
MS_HITS_DF = MS_HITS_DF.loc[MS_HITS_DF.peptide.str.len() <= 15]
......
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