old_contents: #!/usr/bin/env python
  import unittest
  import subprocess
  
  class TestSimpleMapping(unittest.TestCase):
      def test_map_1_read(self):
          subprocess.run(['python', 'bin/sillymap', 'index', 'tests/test_data/reference.fa'])
          result = subprocess.run(['python', 'bin/sillymap', 'map', 'tests/test_data/reference.fa', 'tests/test_data/reads_1.fq'], stdout=subprocess.PIPE)
          self.assertEqual(result.stdout, b'read1,5\n')
  
      def test_map_5_reads(self):
          subprocess.run(['python', 'bin/sillymap', 'index', 'tests/test_data/reference.fa'])
          result = subprocess.run(['python', 'bin/sillymap', 'map', 'tests/test_data/reference.fa', 'tests/test_data/reads_2.fq'], stdout=subprocess.PIPE)
          self.assertEqual(result.stdout, b'read1,5\nread2,0\nread3,10\nread4,15\nread5,5\n')
  
  if __name__ == '__main__':
      unittest.main()
  
new_contents: #!/usr/bin/env python
  import unittest
  import subprocess
  
  class TestSimpleMapping(unittest.TestCase):
      def test_map_1_read(self):
          subprocess.run(['python', 'bin/sillymap', 'index', 'tests/test_data/reference.fa'])
          result = subprocess.run(['python', 'bin/sillymap', 'map', 'tests/test_data/reference.fa', 'tests/test_data/reads_1.fq'], stdout=subprocess.PIPE)
          subprocess.run(['rm', 'tests/test_data/reference.fa.silly'])
          self.assertEqual(result.stdout, b'read1,5\n')
  
      def test_map_5_reads(self):
          subprocess.run(['python', 'bin/sillymap', 'index', 'tests/test_data/reference.fa'])
          result = subprocess.run(['python', 'bin/sillymap', 'map', 'tests/test_data/reference.fa', 'tests/test_data/reads_2.fq'], stdout=subprocess.PIPE)
          subprocess.run(['rm', 'tests/test_data/reference.fa.silly'])
          self.assertEqual(result.stdout, b'read1,5\nread2,0\nread3,10\nread4,15\nread5,5\n')
  
  if __name__ == '__main__':
      unittest.main()
  
subject: Remove index file created in test