old_contents: import logging
  logging.getLogger('matplotlib').disabled = True
  logging.getLogger('tensorflow').disabled = True
  
  import tempfile
  import os
  
  import pandas
  from numpy.testing import assert_equal
  
  from mhcflurry import predict_command
  
  from mhcflurry.testing_utils import cleanup, startup
  teardown = cleanup
  setup = startup
  
  TEST_CSV = '''
  Allele,Peptide,Experiment
  HLA-A0201,SYNFEKKL,17
  HLA-B4403,AAAAAAAAA,17
  HLA-B4403,PPPPPPPP,18
  '''.strip()
  
  
  def test_csv():
      args = ["--allele-column", "Allele", "--peptide-column", "Peptide"]
      deletes = []
      try:
          with tempfile.NamedTemporaryFile(delete=False, suffix=".csv") as fd:
              fd.write(TEST_CSV.encode())
              deletes.append(fd.name)
          fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
          deletes.append(fd_out.name)
          full_args = [fd.name] + args + ["--out", fd_out.name]
          print("Running with args: %s" % full_args)
          predict_command.run(full_args)
          result = pandas.read_csv(fd_out.name)
          print(result)
          assert not result.isnull().any().any()
      finally:
          for delete in deletes:
              os.unlink(delete)
  
      assert_equal(result.shape, (3, 7))
  
  
  def test_no_csv():
      args = [
          "--alleles", "HLA-A0201", "H-2-Kb",
          "--peptides", "SIINFEKL", "DENDREKLLL", "PICKLEEE",
          "--prediction-column-prefix", "mhcflurry1_",
          "--affinity-only",
      ]
  
      deletes = []
      try:
          fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
          deletes.append(fd_out.name)
          full_args = args + ["--out", fd_out.name]
          print("Running with args: %s" % full_args)
          predict_command.run(full_args)
          result = pandas.read_csv(fd_out.name)
          print(result)
      finally:
          for delete in deletes:
              os.unlink(delete)
  
      print(result)
      assert_equal(len(result), 6)
      sub_result1 = result.loc[result.peptide == "SIINFEKL"].set_index("allele")
      print(sub_result1)
      assert (
          sub_result1.loc["H-2-Kb"].mhcflurry1_affinity <
          sub_result1.loc["HLA-A0201"].mhcflurry1_affinity)
  
new_contents: import logging
  logging.getLogger('matplotlib').disabled = True
  logging.getLogger('tensorflow').disabled = True
  
  import tempfile
  import os
  
  import pandas
  from numpy.testing import assert_equal
  
  from mhcflurry import predict_command
  
  from mhcflurry.testing_utils import cleanup, startup
  teardown = cleanup
  setup = startup
  
  TEST_CSV = '''
  Allele,Peptide,Experiment
  HLA-A0201,SYNFEKKL,17
  HLA-B4403,AAAAAAAAA,17
  HLA-B4403,PPPPPPPP,18
  '''.strip()
  
  
  def test_csv():
      args = ["--allele-column", "Allele", "--peptide-column", "Peptide"]
      deletes = []
      try:
          with tempfile.NamedTemporaryFile(delete=False, suffix=".csv") as fd:
              fd.write(TEST_CSV.encode())
              deletes.append(fd.name)
          fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
          deletes.append(fd_out.name)
          full_args = [fd.name] + args + ["--out", fd_out.name]
          print("Running with args: %s" % full_args)
          predict_command.run(full_args)
          result = pandas.read_csv(fd_out.name)
          print(result)
          assert not result.isnull().any().any()
      finally:
          for delete in deletes:
              os.unlink(delete)
  
      assert_equal(result.shape, (3, 8))
  
  
  def test_no_csv():
      args = [
          "--alleles", "HLA-A0201", "H-2-Kb",
          "--peptides", "SIINFEKL", "DENDREKLLL", "PICKLEEE",
          "--prediction-column-prefix", "mhcflurry1_",
          "--affinity-only",
      ]
  
      deletes = []
      try:
          fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
          deletes.append(fd_out.name)
          full_args = args + ["--out", fd_out.name]
          print("Running with args: %s" % full_args)
          predict_command.run(full_args)
          result = pandas.read_csv(fd_out.name)
          print(result)
      finally:
          for delete in deletes:
              os.unlink(delete)
  
      print(result)
      assert_equal(len(result), 6)
      sub_result1 = result.loc[result.peptide == "SIINFEKL"].set_index("allele")
      print(sub_result1)
      assert (
          sub_result1.loc["H-2-Kb"].mhcflurry1_affinity <
          sub_result1.loc["HLA-A0201"].mhcflurry1_affinity)
  
subject: fix test