def setUp(self):
self.left_flanking = '/Users/jane/Desktop/ismap_v2/gold_standard_files/9262_1#29_ISAba1_left_final.fastq'
self.empty_right_flanking = '/Users/jane/Desktop/ismap_v2/gold_standard_files/empty_files/9262_1#29_ISAba1_right_final.fastq'
ref_seqs = ismap_v2.get_sequences(['/Users/jane/Desktop/ismap_v2/refs/CP010781.gbk'], 'genbank')
self.ref = ref_seqs[0]
self.query_single = ['/Users/jane/Desktop/ismap_v2/queries/ISAba1.fasta']
self.query_records = ismap_v2.get_sequences(self.query_single, 'fasta')
self.is_query = self.query_records[0]
self.sample = '9262_1#29'
self.main_out_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/'
self.tmp_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/ISAba1/tmp'
self.out_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/ISAba1/'
# make the output directories
if not os.path.exists(self.tmp_folder):
os.makedirs(self.tmp_folder)
def setUp(self):
self.left_flanking = '/Users/jane/Desktop/ismap_v2/gold_standard_files/9262_1#29_ISAba1_left_final.fastq'
self.empty_right_flanking = '/Users/jane/Desktop/ismap_v2/gold_standard_files/empty_files/9262_1#29_ISAba1_right_final.fastq'
ref_seqs = ismap_v2.get_sequences(
['/Users/jane/Desktop/ismap_v2/refs/CP010781.gbk'], 'genbank')
self.ref = ref_seqs[0]
self.query_single = [
'/Users/jane/Desktop/ismap_v2/queries/ISAba1.fasta'
]
self.query_records = ismap_v2.get_sequences(self.query_single, 'fasta')
self.is_query = self.query_records[0]
self.sample = '9262_1#29'
self.main_out_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/'
self.tmp_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/ISAba1/tmp'
self.out_folder = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29/ISAba1/'
# make the output directories
if not os.path.exists(self.tmp_folder):
os.makedirs(self.tmp_folder)
def setUp(self):
# set up reads
self.test_reads = [pathlib.Path('/Users/jane/Desktop/ismap_v2/reads/9262_1#29_1.fastq.gz'),
pathlib.Path('/Users/jane/Desktop/ismap_v2/reads/9262_1#29_2.fastq.gz')]
self.read_groups = read_grouping.group_reads(self.test_reads)
self.sample = self.read_groups.paired[0]
# set up IS query
self.query_single = ['/Users/jane/Desktop/ismap_v2/queries/ISAba1.fasta']
self.query_records = ismap_v2.get_sequences(self.query_single, 'fasta')
self.is_query = self.query_records[0]
# set up output
self.output = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29'
def test_get_seqs_01(self):
# check that when we give valid files, we return a list object
self.assertIsInstance(ismap_v2.get_sequences(self.query_single, 'fasta'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.query_list, 'fasta'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.query_multi, 'fasta'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.genome_single, 'genbank'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.genome_list, 'genbank'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.genome_multi, 'genbank'), list)
def setUp(self):
# set up reads
self.test_reads = [
pathlib.Path(
'/Users/jane/Desktop/ismap_v2/reads/9262_1#29_1.fastq.gz'),
pathlib.Path(
'/Users/jane/Desktop/ismap_v2/reads/9262_1#29_2.fastq.gz')
]
self.read_groups = read_grouping.group_reads(self.test_reads)
self.sample = self.read_groups.paired[0]
# set up IS query
self.query_single = [
'/Users/jane/Desktop/ismap_v2/queries/ISAba1.fasta'
]
self.query_records = ismap_v2.get_sequences(self.query_single, 'fasta')
self.is_query = self.query_records[0]
# set up output
self.output = '/Users/jane/Desktop/ismap_v2/test_results/9262_1#29'
def test_get_seqs_01(self):
# check that when we give valid files, we return a list object
self.assertIsInstance(
ismap_v2.get_sequences(self.query_single, 'fasta'), list)
self.assertIsInstance(ismap_v2.get_sequences(self.query_list, 'fasta'),
list)
self.assertIsInstance(
ismap_v2.get_sequences(self.query_multi, 'fasta'), list)
self.assertIsInstance(
ismap_v2.get_sequences(self.genome_single, 'genbank'), list)
self.assertIsInstance(
ismap_v2.get_sequences(self.genome_list, 'genbank'), list)
self.assertIsInstance(
ismap_v2.get_sequences(self.genome_multi, 'genbank'), list)
def test_get_seqs_02(self):
# check that if the list is empty, we print a useful error
with self.assertRaises(ismap_v2.NoSeqError):
ismap_v2.get_sequences([], 'fasta')
def test_get_seqs_02(self):
# check that if the list is empty, we print a useful error
with self.assertRaises(ismap_v2.NoSeqError):
ismap_v2.get_sequences([], 'fasta')