def test_generate_intron_fasta_no_transcript(self):
with self.assertRaises(Exception):
out_path = os.path.join(
tempfile.gettempdir(), '{}.fa'.format(uuid.uuid4())
)
fasta.generate_intron_fasta(
self.sorted_fasta_path, self.gtf_no_transcript, out_path
)
def test_generate_intron_fasta(self):
out_path = os.path.join(self.temp_dir, '{}.fa'.format(uuid.uuid4()))
self.assertEqual(
out_path,
fasta.generate_intron_fasta(self.sorted_fasta_path,
self.sorted_gtf_path,
out_path,
flank=1))
with open(out_path, 'r') as f, open(self.split_intron_fasta_path,
'r') as split:
self.assertEqual(f.read(), split.read())
def test_generate_intron_fasta_with_chromosomes(self):
out_path = os.path.join(
tempfile.gettempdir(), '{}.fa'.format(uuid.uuid4())
)
self.assertEqual(
out_path,
fasta.generate_intron_fasta(
self.sorted_fasta_path,
self.sorted_gtf_path,
out_path,
chromosomes={'1'},
flank=1
)
)
with open(out_path, 'r') as f, open(self.partial_intron_fasta_path,
'r') as split:
self.assertEqual(f.read(), split.read())
def test_generate_intron_fasta_no_exon(self):
with self.assertRaises(Exception):
out_path = os.path.join(self.temp_dir,
'{}.fa'.format(uuid.uuid4()))
fasta.generate_intron_fasta(self.sorted_fasta_path,
self.gtf_no_exon, out_path)