def test_create_msa_slice_from_sam_slice(self):
"""
Tests that the sam_handler.create_msa_slice_from_sam() slices properly
"""
ACTUAL_TEST_MERGE_FULL_MSA_FASTA = TEST_DIR + os.sep + os.path.basename(TEST_MERGE_FASTQ).replace(".fq", ".msa.fasta")
TEST_MERGE_SAM = TEST_DIR + os.sep + os.path.basename(TEST_MERGE_FASTQ).replace(".fq", ".sam")
self.__write_sam_testcase(self.merge_testcases, TEST_MERGE_SAM)
self.assertTrue(os.path.exists(TEST_MERGE_SAM) and os.path.getsize(TEST_MERGE_SAM) > 0,
"Expected test case sam for merging records " + TEST_MERGE_SAM + " does not exist or is empty")
actual_written = sam.sam_handler.create_msa_slice_from_sam(sam_filename=TEST_MERGE_SAM,
ref=self.merge_testcases[0].target_ref,
out_fasta_filename=ACTUAL_TEST_MERGE_FULL_MSA_FASTA,
mapping_cutoff=MAPQ_CUTOFF,
read_qual_cutoff=READ_QUAL_CUTOFF,
max_prop_N=1.0, breadth_thresh=MIN_WINDOW_BREADTH_COV_FRACTION,
start_pos=self.merge_testcases[0].slice_start,
end_pos=self.merge_testcases[0].slice_end, do_insert_wrt_ref=True,
do_mask_stop_codon=True)
self.assertTrue(os.path.exists(ACTUAL_TEST_MERGE_FULL_MSA_FASTA) and os.path.getsize(ACTUAL_TEST_MERGE_FULL_MSA_FASTA) > 0,
ACTUAL_TEST_MERGE_FULL_MSA_FASTA + " doesn't exist or is empty")
actual_header2seq = Utility.get_seq_dict(ACTUAL_TEST_MERGE_FULL_MSA_FASTA)
expected_written = 0
for testcase in self.merge_testcases:
expected_seq, expected_qual = testcase.get_sliced_merged_read(slice_start_pos_wrt_ref_1based=testcase.slice_start,
slice_end_pos_wrt_ref_1based=testcase.slice_end,
do_pad_wrt_slice=True, do_insert_wrt_ref=True, do_mask_stop_codon=True)
actual_seq = actual_header2seq.get(testcase.read_name, None)
slice_len = self.merge_testcases[0].slice_end - self.merge_testcases[0].slice_start + 1
if float(expected_seq.count("N") + expected_seq.count("-")) / slice_len > (1.0- MIN_WINDOW_BREADTH_COV_FRACTION):
self.assertIsNone(actual_seq,
"Expect read " + testcase.read_name + " should not be in " + ACTUAL_TEST_MERGE_FULL_MSA_FASTA)
else:
expected_written += 1
self.assertEqual(expected_seq, actual_seq,
"Expected {} but got {} for testcase {}".format(expected_seq, actual_seq, testcase.read_name))
self.assertEqual(expected_written, actual_written,
"Expect total written seq {} but got {} from {}".format(expected_written, actual_written, ACTUAL_TEST_MERGE_FULL_MSA_FASTA))
def test_create_msa_slice_from_sam_maxpropN(self):
"""
Tests that the sam_handler.create_msa_slice_from_sam() filters out sequences that have too many N's or gaps
"""
# We only care that the sequences are filtered by fraction of N's.
# We don't care about breadth thresholds or slicing.
ACTUAL_TEST_MERGE_FULL_MSA_FASTA = TEST_DIR + os.sep + os.path.basename(TEST_MERGE_FASTQ).replace(".fq", ".msa.fasta")
TEST_MERGE_SAM = TEST_DIR + os.sep + os.path.basename(TEST_MERGE_FASTQ).replace(".fq", ".sam")
self.__write_sam_testcase(self.merge_testcases, TEST_MERGE_SAM)
self.assertTrue(os.path.exists(TEST_MERGE_SAM) and os.path.getsize(TEST_MERGE_SAM) > 0,
"Expected test case sam for merging records " + TEST_MERGE_SAM + " does not exist or is empty")
actual_written = sam.sam_handler.create_msa_slice_from_sam(sam_filename=TEST_MERGE_SAM,
ref=self.merge_testcases[0].target_ref,
out_fasta_filename=ACTUAL_TEST_MERGE_FULL_MSA_FASTA,
mapping_cutoff=MAPQ_CUTOFF,
read_qual_cutoff=READ_QUAL_CUTOFF,
max_prop_N=MAX_PROP_N, breadth_thresh=0,
start_pos=0, end_pos=0, do_insert_wrt_ref=True,
do_mask_stop_codon=True)
self.assertTrue(os.path.exists(ACTUAL_TEST_MERGE_FULL_MSA_FASTA) and os.path.getsize(ACTUAL_TEST_MERGE_FULL_MSA_FASTA) > 0,
ACTUAL_TEST_MERGE_FULL_MSA_FASTA + " doesn't exist or is empty")
actual_header2seq = Utility.get_seq_dict(ACTUAL_TEST_MERGE_FULL_MSA_FASTA)
expected_written = 0
for testcase in self.merge_testcases:
expected_seq, expected_qual = testcase.get_sliced_merged_read(slice_start_pos_wrt_ref_1based=None, slice_end_pos_wrt_ref_1based=None,
do_pad_wrt_slice=True, do_insert_wrt_ref=True, do_mask_stop_codon=True)
actual_seq = actual_header2seq.get(testcase.read_name, None)
if expected_seq.count("N") / float(len(expected_seq)) > MAX_PROP_N:
self.assertIsNone(actual_seq,
"Expect read " + testcase.read_name + " should not be in " + ACTUAL_TEST_MERGE_FULL_MSA_FASTA)
else:
expected_written += 1
self.assertEqual(expected_seq, actual_seq,
"Expected {} but got {} for testcase {}".format(expected_seq, actual_seq, testcase.read_name))
self.assertEqual(expected_written, actual_written,
"Expect total written seq {} but got {} from {}".format(expected_written, actual_written, ACTUAL_TEST_MERGE_FULL_MSA_FASTA))
