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)