Python to_fastg Examples

Example #1

File: tasks_test.py Project: martinghunt/Fastaq

 def test_to_fastg_ids_file(self):
     '''Test to_fastg when ids in a file'''
     infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta')
     tmpfile = 'tmp.to_fastg.fastg'
     expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg')
     ids_file = os.path.join(data_dir, 'tasks_test_to_fastg.ids_to_circularise')
     tasks.to_fastg(infile, tmpfile, circular=ids_file)
     self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
     os.unlink(tmpfile)

Example #2

File: tasks_test.py Project: sanger-pathogens/Fastaq

 def test_to_fastg_ids_file(self):
     '''Test to_fastg when ids in a file'''
     infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta')
     tmpfile = 'tmp.to_fastg.fastg'
     expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg')
     ids_file = os.path.join(data_dir, 'tasks_test_to_fastg.ids_to_circularise')
     tasks.to_fastg(infile, tmpfile, circular=ids_file)
     self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
     os.unlink(tmpfile)

Example #3

File: tasks_test.py Project: martinghunt/Fastaq

 def test_to_fastg_ids_set(self):
     '''Test to_fastg when ids are a set'''
     infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta')
     tmpfile = 'tmp.to_fastg.fastg'
     expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg')
     ids = {'seq2'}
     tasks.to_fastg(infile, tmpfile, circular=ids)
     self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
     os.unlink(tmpfile)

Example #4

File: tasks_test.py Project: sanger-pathogens/Fastaq

 def test_to_fastg_ids_set(self):
     '''Test to_fastg when ids are a set'''
     infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta')
     tmpfile = 'tmp.to_fastg.fastg'
     expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg')
     ids = {'seq2'}
     tasks.to_fastg(infile, tmpfile, circular=ids)
     self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
     os.unlink(tmpfile)