From c64db7772a697084b1d992a8dbec046a52c0ab42 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 6 Mar 2020 17:44:51 -0500
Subject: [PATCH] Delete AuxiliaryInput class
---
mhcflurry/auxiliary_input.py | 109 -----------------------------------
test/test_auxiliary_input.py | 39 -------------
2 files changed, 148 deletions(-)
delete mode 100644 mhcflurry/auxiliary_input.py
delete mode 100644 test/test_auxiliary_input.py
diff --git a/mhcflurry/auxiliary_input.py b/mhcflurry/auxiliary_input.py
deleted file mode 100644
index 982a1863..00000000
--- a/mhcflurry/auxiliary_input.py
+++ /dev/null
@@ -1,109 +0,0 @@
-import numpy
-from numpy.testing import assert_equal
-import pandas
-
-AUXILIARY_FEATURES = {}
-
-
-class AuxiliaryInputEncoder(object):
- def __init__(self, alleles=None, peptides=None):
- if alleles is not None:
- alleles = numpy.array(
- alleles, copy=False).reshape((len(alleles), -1))
- assert_equal(alleles.ndim, 2)
- if peptides is not None:
- peptides = numpy.array(peptides, copy=False)
- assert_equal(peptides.ndim, 1)
- if alleles is not None and peptides is not None:
- assert_equal(alleles.shape[0], len(peptides))
-
- self.alleles_shape = alleles.shape if alleles is not None else None
- self.alleles_flat = alleles.flatten() if alleles is not None else None
- self.peptides = numpy.repeat(
- peptides,
- self.alleles_shape[1] if alleles is not None else 1
- ) if peptides is not None else None
-
- @staticmethod
- def fill_dataframe(result_df, features, feature_parameters={}):
- for feature in features:
- obj = AUXILIARY_FEATURES[feature](
- **feature_parameters.get(feature, {}))
- obj(result_df)
-
- @classmethod
- def get_columns(cls, features, feature_parameters={}):
- result_df = pandas.DataFrame(
- {"allele": [], "peptide": []}, dtype=str)
- cls.fill_dataframe(result_df, features, feature_parameters)
- del result_df["allele"]
- del result_df["peptide"]
- return result_df.columns.tolist()
-
- @staticmethod
- def split_features(how, features, feature_parameters={}):
- predicate = None
- if how == "peptide_independent":
- predicate = lambda obj: not obj.requires_peptides
- elif how == "allele_independent":
- predicate = lambda obj: not obj.requires_alleles
- else:
- raise NotImplementedError("Unsupported 'how' value", how )
-
- matching = []
- non_matching = []
- for feature in features:
- obj = AUXILIARY_FEATURES[feature](
- **feature_parameters.get(feature, {}))
- if predicate(obj):
- matching.append(feature)
- else:
- non_matching.append(feature)
- return (matching, non_matching)
-
- def get_array(self, features, feature_parameters={}):
- result_df = pandas.DataFrame()
- if self.alleles_flat is not None:
- result_df["allele"] = self.alleles_flat
- if self.peptides is not None:
- result_df["peptide"] = self.peptides
-
- for feature in features:
- obj = AUXILIARY_FEATURES[feature](
- **feature_parameters.get(feature, {}))
- if obj.requires_alleles and "allele" not in result_df.columns:
- raise ValueError("%s requires alleles" % obj.name)
- if obj.requires_peptides and "peptide" not in result_df.columns:
- raise ValueError("%s requires peptides" % obj.name)
- obj(result_df)
- if "allele" in result_df.columns:
- del result_df["allele"]
- if "peptide" in result_df.columns:
- del result_df["peptide"]
- result = numpy.reshape(
- result_df.values, self.alleles_shape + (-1,)).astype("float32")
- assert not numpy.isnan(result).any()
- return result
-
-
-class AuxiliaryInputFeature(object):
- name = None
- requires_alleles = False
- requires_peptides = False
-
- def __call__(self, *args, **kwargs):
- raise NotImplementedError()
-
-
-class Gene(AuxiliaryInputFeature):
- name = "gene"
- requires_alleles = True
-
- def __call__(self, result_df):
- result_df["gene:HLA-A"] = (
- result_df.allele.fillna("").str.startswith("HLA-A"))
- result_df["gene:HLA-B"] = (
- result_df.allele.fillna("").str.startswith("HLA-B"))
-
-
-AUXILIARY_FEATURES[Gene.name] = Gene
diff --git a/test/test_auxiliary_input.py b/test/test_auxiliary_input.py
deleted file mode 100644
index 741e2e2d..00000000
--- a/test/test_auxiliary_input.py
+++ /dev/null
@@ -1,39 +0,0 @@
-from mhcflurry import auxiliary_input
-from nose.tools import eq_
-from numpy.testing import assert_equal
-import numpy
-import pandas
-
-
-def test_gene():
- alleles1 = [
- "HLA-A*02:01",
- "HLA-A*02:01",
- "HLA-B*07:02",
- "HLA-B*07:02",
- "HLA-C*03:01",
- "HLA-C*02:01",
- ]
- alleles2 = [
- "HLA-A*03:01",
- "HLA-A*20:01",
- "HLA-B*03:01",
- "HLA-C*03:01",
- "HLA-C*07:01",
- "HLA-C*02:01",
- ]
-
- encoder = auxiliary_input.AuxiliaryInputEncoder(
- alleles=[alleles1, alleles2])
- result = encoder.get_array(features=["gene"])
- print(result)
- assert_equal(
- result,
- [
- [
- [1, 0], [1, 0], [0, 1], [0, 1], [0, 0], [0, 0],
- ],
- [
- [1, 0], [1, 0], [0, 1], [0, 0], [0, 0], [0, 0],
- ],
- ])
\ No newline at end of file
--
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