def test_input_file_does_not_exists(self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
input_fasta = execution_path + "/file_that_does_not_exists.fasta"
output = execution_path + self.MIX_CODING_CASES
sys.argv = [sys.argv[0], "-input", input_fasta, "-output", output]
with self.assertRaises(IOError):
codon_optimizer()
def test_log_creation(self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
input_fasta = execution_path + self.CODING_CASES
output = execution_path + self.OUTPUT_FOR_CODING_CASES
log = execution_path + "/output/codon_optimizer.log"
sys.argv = [sys.argv[0], "-input", input_fasta, "-output", output]
codon_optimizer()
self.assertTrue(os.path.exists(log))
def test_input_output_not_coding_sequence(self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
input_fasta = execution_path + "/cases/input_not_coding_sequences.fa"
output = execution_path + "/output/not_coding_seq_codon_optimized.fasta"
sys.argv = [sys.argv[0], "-input", input_fasta, "-output", output]
codon_optimizer()
self.assertFalse(os.path.exists(output))
def test_input_output_coding_sequence(self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
reference_output_fasta = execution_path + "/cases/coding_seq_codon_optimized_formatted.fasta"
input_fasta = execution_path + "/cases/input_coding_sequences.fa"
output = execution_path + "/output/coding_seq_codon_optimized.fasta"
sys.argv = [sys.argv[0], "-input", input_fasta, "-output", output]
codon_optimizer()
a = open(reference_output_fasta, 'r')
b = open(output, 'r')
a_read = a.read()
b_read = b.read()
a.close()
b.close()
self.assertTrue(a_read == b_read)
def test_input_output_mix_coding_not_coding_sequence(self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
reference_output_fasta = execution_path + self.MIX_CODING_CASES
input_fasta = execution_path + self.CODING_CASES
output = execution_path + self.OUTPUT_FOR_CODING_CASES
sys.argv = [sys.argv[0], "-input", input_fasta, "-output", output]
codon_optimizer()
a = open(reference_output_fasta, 'r')
b = open(output, 'r')
a_read = a.read()
b_read = b.read()
a.close()
b.close()
self.assertTrue(a_read == b_read)
def test_input_output_mix_coding_not_coding_sequence_different_ref_freqtab(
self):
execution_path = os.path.dirname(__file__)
os.chdir(execution_path)
reference_output_fasta = execution_path + self.MIX_CODING_CASES
input_fasta = execution_path + self.CODING_CASES
output = execution_path + self.OUTPUT_FOR_CODING_CASES
reffreqtab = execution_path + "/cases/Mus_musculus_codon_frequency.csv"
sys.argv = [
sys.argv[0], "-input", input_fasta, "-output", output,
"-reffreqtab", reffreqtab
]
codon_optimizer()
a = open(reference_output_fasta, 'r')
b = open(output, 'r')
a_read = a.read()
b_read = b.read()
a.close()
b.close()
self.assertFalse(a_read == b_read)