old_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #       http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """
  Make sure all binding predictors give a high IC50 and percentile rank.
  """
  import mhctools
  
  mhc_classes = [
      mhctools.NetMHCcons,
      mhctools.NetMHCpan,
      mhctools.NetMHCcons,
      mhctools.NetMHC,
  ]
  
  def test_MAGE_epitope():
      """
      Test the A1 MAGE epitope from
          Identification of a Titin-Derived HLA-A1-Presented Peptide
          as a Cross-Reactive Target for Engineered MAGE A3-Directed
          T Cells
      """
      for mhc_class in mhc_classes:
          mhc_model = mhc_class("HLA-A*01:01", epitope_lengths=9)
          epitope = mhc_model.predict("ESDPIVAQY")[0]
          assert epitope.value < 500, "Expected %s to have IC50 < 500nM" % epitope
  
  def test_HIV_epitope():
      """
      Test the A2 HIV epitope from
          The HIV-1 HLA-A2-SLYNTVATL Is a Help-Independent CTL Epitope
      """
      for mhc_class in mhc_classes:
          mhc_model = mhc_class("HLA-A*02:01", epitope_lengths=9)
          epitope = mhc_model.predict("SLYNTVATL")[0]
          assert epitope.percentile_rank <= 4.0, \
              "Expected %s to have percentile rank <= 3.0" % str(epitope)
  
new_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #       http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """
  Make sure all binding predictors give a high IC50 and percentile rank.
  """
  import mhctools
  
  mhc_classes = [
      mhctools.NetMHCcons,
      mhctools.NetMHCpan,
      mhctools.NetMHCcons,
      mhctools.NetMHC,
  ]
  
  def test_MAGE_epitope():
      """
      Test the A1 MAGE epitope from
          Identification of a Titin-Derived HLA-A1-Presented Peptide
          as a Cross-Reactive Target for Engineered MAGE A3-Directed
          T Cells
      """
      for mhc_class in mhc_classes:
          mhc_model = mhc_class("HLA-A*01:01", epitope_lengths=9)
          epitope = mhc_model.predict("ESDPIVAQY")[0]
          assert epitope.value < 500, "Expected %s to have IC50 < 500nM" % epitope
  
  def test_HIV_epitope():
      """
      Test the A2 HIV epitope from
          The HIV-1 HLA-A2-SLYNTVATL Is a Help-Independent CTL Epitope
      """
      for mhc_class in mhc_classes:
          mhc_model = mhc_class("HLA-A*02:01", epitope_lengths=9)
          epitope = mhc_model.predict("SLYNTVATL")[0]
          assert epitope.value < 500, \
              "Expected %s to have IC50 < 500nM" % (epitope,)
  
subject: Fix merge error in a test