def test_save_emptyReporterReturnsHeadersOnly(self):
delim = "\t"
reporter = RecallReporter(classifiers=[RecallClassifier()],
delim=delim)
fh = StringIO(newline="")
report = reporter._generate_report()
reporter.save_report(report, fh)
fh.seek(0)
actual = fh.read()
expected = delim.join(reporter.columns) + "\n"
assert actual == expected
def test_save_reporterWithTwoClassifiersWritesTwoSamplesWithTwoRows(self):
primary_correct_record = create_correct_primary_sam_record()
suppl_incorrect_record = create_incorrect_supplementary_sam_record()
delim = ","
classifier1 = create_classifier_with_two_entries(RecallClassifier)
sample = "sample"
classifier1.name = sample
classifier2 = create_classifier_with_two_entries(RecallClassifier)
sample2 = "sample2"
classifier2.name = sample2
reporter = RecallReporter(classifiers=[classifier1, classifier2],
delim=delim)
fh = StringIO(newline="")
report = reporter._generate_report()
reporter.save_report(report, fh)
fh.seek(0)
actual = fh.read()
expected_data = []
for s in [sample, sample2]:
for assessment, record in [
(AlignmentAssessment.PRIMARY_CORRECT, primary_correct_record),
(AlignmentAssessment.SUPPLEMENTARY_INCORRECT,
suppl_incorrect_record),
]:
expected_data.append(
[s, record.query_name, record.reference_name, assessment])
expected = StringIO(newline="")
pd.DataFrame(
expected_data,
columns=[
"sample",
"query_probe_header",
"ref_probe_header",
"classification",
],
).to_csv(expected, sep=delim, header=True, index=False)
expected.seek(0)
expected = expected.read()
assert actual == expected
gt_conf_percentiles = snakemake.params.gt_conf_percentiles
# API usage
logging.info(f"Creating masker from {mask_filepath}")
with open(mask_filepath) as bed:
masker = RecallMasker.from_bed(bed)
for sam_filepath, variant_call_recall_report, gt_conf_percentile in zip(
sams_filepath, variant_call_recall_reports, gt_conf_percentiles):
logging.info(f"Masking SAM records")
with pysam.AlignmentFile(sam_filepath) as sam:
records = masker.filter_records(sam)
logging.info("Creating classifier")
classifier = RecallClassifier(sam=records, name=sample_id)
logging.info("Creating reporter")
reporter = RecallReporter(classifiers=[classifier])
logging.info("Generating report")
# TODO: we are passing gt_conf_percentile (values in [0, 100, 1]) as gt_conf
# TODO: fix this? It does not really matter as we use step gt (which is gt_conf_percentile) anyway later
report = reporter.generate_report(gt_conf_percentile)
# output
logging.info("Saving report")
with open(variant_call_recall_report, "w") as output:
reporter.save_report(report, output)
logging.info("Done")