def test_basic(self):
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "filter_subread"
cmd = "{e} --debug -o {o} -r {r} {csv}".format(
e=exe,
csv=self.filtered_subread_summary_csv,
r=report_json,
o=output_dir)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
with open(report_json, 'r') as f:
d = json.loads(f.read())
report = dict_to_report(d)
log.info("deserialized report:")
log.info(pformat(report.to_dict()))
self.assertIsNotNone(isinstance(report, Report))
# Cleanup
self.assertTrue(os.path.exists(report_json))
os.remove(report_json)
def test_basic(self):
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "filter_subread"
cmd = "{e} --debug -o {o} -r {r} {csv}".format(
e=exe, csv=self.filtered_subread_summary_csv, r=report_json, o=output_dir
)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
with open(report_json, "r") as f:
d = json.loads(f.read())
report = dict_to_report(d)
log.info("deserialized report:")
log.info(pformat(report.to_dict()))
self.assertIsNotNone(isinstance(report, Report))
# Cleanup
self.assertTrue(os.path.exists(report_json))
os.remove(report_json)
def test_basic(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "amplicon_analysis_consensus_report"
cmd = "{e} --debug {csv} {r}".format(e=exe, csv=self.file_name, r=report_json)
exit_code = run_backticks(cmd, 1)
# Assert the job failed
self.assertEqual(exit_code, 1)
def setUpClass(cls):
cls.report_constants = pbreports.report.isoseq_cluster.Constants
cls.results_dir = tempfile.mkdtemp(prefix="isoseq_results_")
cls.input_fasta = os.path.join(_DATA_DIR, 'isoseq_flnc.fasta')
cls.output_summary_txt = os.path.join(_DATA_DIR, 'isoseq_cluster_summary.txt')
cls.report_json = os.path.join(cls.results_dir, "isoseq_cluster.json")
_d = dict(o=cls.results_dir, f=cls.input_fasta, s=cls.output_summary_txt, j=cls.report_json)
cmd = 'isoseq_cluster_report --debug {f} {s} {j}'.format(**_d)
cls.code = run_backticks(cmd)
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
cmd = "python -m pbreports.report.variants {o} {r} {c} {a} {v}".format(
o=self._output_dir, r="rpt.json", c=self.REFERENCE, a=self.ALIGNMENT_SUMMARY, v=self.VARIANTS_GFF
)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(op.exists(op.join(self._output_dir, "rpt.json")))
def test_basic(self):
t = tempfile.NamedTemporaryFile(suffix="_motif_report.json", delete=False)
t.close()
json_report = t.name
output_dir = os.path.dirname(json_report)
_d = dict(g=_MOTIF_GFF, c=_MOTIF_SUMMARY_CSV, j=json_report, d=output_dir, e=EXE)
cmd_str = "{e} {g} {c} {j}".format(**_d)
rcode = run_backticks(cmd_str)
self.assertEqual(rcode, 0, "Exit code '{o}' for command '{c}'".format(o=rcode, c=cmd_str))
def test_exit_code_0_fasta(self):
"""
Like a cram test. Assert exits with 0 with fasta.
"""
cmd = 'python -m pbreports.report.variants {o} {r} {c} {a} {v}'.format(
o=self._output_dir, r='rpt.json', c=self._get_reference_fasta(),
a=self.ALIGNMENT_SUMMARY,
v=self.VARIANTS_GFF)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(op.exists(op.join(self._output_dir, 'rpt.json')))
def test_basic(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "amplicon_analysis_consensus_report"
cmd = "{e} --debug {csv} {r}".format(e=exe,
csv=self.file_name,
r=report_json)
exit_code = run_backticks(cmd, 1)
# Assert the job failed
self.assertEqual(exit_code, 1)
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
cmd = 'python -m pbreports.report.variants {r} {c} {a} {v}'.format(
r='rpt.json',
c=self.REFERENCE,
a=self.ALIGNMENT_SUMMARY,
v=self.VARIANTS_GFF)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue('rpt.json')
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
j = 'rpt.json'
cmd = 'python -m pbreports.report.top_variants {j} {g} {r}'.format(
g=gff, r=ref, j=j)
log.info(cmd)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
cmd = 'python -m pbreports.report.variants {r} {c} {a} {v}'.format(
r='rpt.json',
c=self.REFERENCE,
a=self.ALIGNMENT_SUMMARY,
v=self.VARIANTS_GFF)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue('rpt.json')
def test_basic(self):
cmd = _to_cmd(self.ALIGNMENTS, self.report_json)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
with open(self.report_json, 'r') as f:
s = json.load(f)
log.info("JsonReport: ")
log.info(pprint.pformat(s, indent=4))
report = dict_to_report(s)
self.assertIsNotNone(report)
self.assertEqual(len(report.tables), 1)
log.info(str(report.tables[0]))
validate_report_metadata(self, report, meta_rpt)
def test_basic(self):
cmd = _to_cmd(self.ALIGNMENTS, self.report_json)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
with open(self.report_json, 'r') as f:
s = json.load(f)
log.info("JsonReport: ")
log.info(pprint.pformat(s, indent=4))
report = dict_to_report(s)
self.assertIsNotNone(report)
self.assertEqual(len(report.tables), 1)
log.info(str(report.tables[0]))
validate_report_metadata(self, report, meta_rpt)
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
j = 'rpt.json'
cmd = 'python -m pbreports.report.top_variants {o} {j} {g} {r}'.format(
o=self._output_dir, g=gff, r=ref, j=j)
log.info(cmd)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(os.path.exists(os.path.join(self._output_dir, j)))
def setUpClass(cls):
cls.report_constants = pbreports.report.isoseq_cluster.Constants
cls.results_dir = tempfile.mkdtemp(prefix="isoseq_results_")
cls.input_fasta = os.path.join(_DATA_DIR, 'isoseq_flnc.fasta')
cls.output_summary_json = os.path.join(_DATA_DIR,
'isoseq_cluster_summary.json')
cls.report_json = os.path.join(cls.results_dir, "isoseq_cluster.json")
_d = dict(o=cls.results_dir,
f=cls.input_fasta,
s=cls.output_summary_json,
j=cls.report_json)
cmd = 'isoseq_cluster_report --debug {f} {s} {j}'.format(**_d)
cls.code = run_backticks(cmd)
def test_exit_code_0(self):
"""
Like a cram test. Assert exits with 0.
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
j = 'rpt.json'
cmd = 'python -m pbreports.report.top_variants {o} {j} {g} {r}'.format(
o=self._output_dir, g=gff, r=ref, j=j)
log.info(cmd)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(os.path.exists(os.path.join(self._output_dir, j)))
def test_basic(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
t.close()
output_csv = t.name
exe = "filter_subread_summary"
cmd = "{e} --debug {r} -o {csv}".format(e=exe, r=self.region_fofn,
csv=output_csv)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
# Cleanup
self.assertTrue(os.path.exists(output_csv))
os.remove(output_csv)
def test_exit_code_0_referenceset(self):
"""
Like a cram test. Assert exits with 0 with ReferenceSet XML
"""
ref_name = op.join(self._output_dir, "refset.xml")
refset = ReferenceSet(self._get_reference_fasta())
refset.write(ref_name)
ref = ref_name
cmd = 'python -m pbreports.report.variants {o} {r} {c} {a} {v}'.format(
o=self._output_dir, r='rpt.json', c=ref, a=self.ALIGNMENT_SUMMARY,
v=self.VARIANTS_GFF)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(op.exists(op.join(self._output_dir, "rpt.json")))
def test_exit_code_0_referenceset(self):
"""
Like a cram test. Assert exits with 0 with ReferenceSet XML
"""
ref_name = op.join(self._output_dir, "refset.xml")
refset = ReferenceSet(self._get_reference_fasta())
refset.write(ref_name)
ref = ref_name
cmd = 'python -m pbreports.report.variants {r} {c} {a} {v}'.format(
r='rpt.json', c=ref, a=self.ALIGNMENT_SUMMARY,
v=self.VARIANTS_GFF)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(op.exists("rpt.json"))
def test_basic(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
t.close()
output_csv = t.name
exe = "filter_subread_summary"
cmd = "{e} --debug {r} -o {csv}".format(e=exe,
r=self.region_fofn,
csv=output_csv)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
# Cleanup
self.assertTrue(os.path.exists(output_csv))
os.remove(output_csv)
def test_integration(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "amplicon_analysis_input_report"
cmd = "{e} --debug {s} {r}".format(e=exe,
s=self.csv_file,
r=report_json)
exit_code = run_backticks(cmd)
self.assertEqual(exit_code, 0)
with open(report_json, 'r') as f:
d = json.loads(f.read())
self.assertIsNotNone(d)
# cleanup
if os.path.exists(report_json):
os.remove(report_json)
def test_exit_code_0_referenceset(self):
"""
Like a cram test. Assert exits with 0 with ReferenceSet XML
"""
ref = self._get_reference_fasta()
ref_name = os.path.join(self._output_dir, "refset.xml")
refset = ReferenceSet(ref)
refset.write(ref_name)
ref = ref_name
j = 'rpt.json'
cmd = 'python -m pbreports.report.top_variants {j} {g} {r}'.format(
g=self.VARIANTS_GFF, r=ref, j=j)
log.info(cmd)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
def test_integration(self):
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
report_json = t.name
exe = "amplicon_analysis_input_report"
cmd = "{e} --debug {s} {r}".format(e=exe,
s=self.csv_file,
r=report_json)
exit_code = run_backticks(cmd)
self.assertEqual(exit_code, 0)
with open(report_json, 'r') as f:
d = json.loads(f.read())
self.assertIsNotNone(d)
# cleanup
if os.path.exists(report_json):
os.remove(report_json)
def test_basic(self):
report_json = tempfile.NamedTemporaryFile(suffix=".json").name
exe = "amplicon_analysis_timing_report"
cmd = "{e} --debug {l} {r}".format(e=exe,
l=self.input_log_file,
r=report_json)
exit_code = run_backticks(cmd)
self.assertEqual(exit_code, 0)
with open(report_json, 'r') as f:
d = json.loads(f.read())
self.assertIsNotNone(d)
# cleanup
if os.path.exists(report_json):
os.remove(report_json)
def test_basic(self):
t = tempfile.NamedTemporaryFile(suffix="_motif_report.json",
delete=False)
t.close()
json_report = t.name
output_dir = os.path.dirname(json_report)
_d = dict(g=_MOTIF_GFF,
c=_MOTIF_SUMMARY_CSV,
j=json_report,
d=output_dir,
e=EXE)
cmd_str = '{e} {g} {c} {j}'.format(**_d)
rcode = run_backticks(cmd_str)
self.assertEqual(
rcode, 0, "Exit code '{o}' for command '{c}'".format(o=rcode,
c=cmd_str))
def test_exit_code_0_referenceset(self):
"""
Like a cram test. Assert exits with 0 with ReferenceSet XML
"""
ref = self._get_reference_fasta()
ref_name = os.path.join(self._output_dir, "refset.xml")
refset = ReferenceSet(ref)
refset.write(ref_name)
ref = ref_name
j = 'rpt.json'
cmd = 'python -m pbreports.report.top_variants {o} {j} {g} {r}'.format(
o=self._output_dir,
g=self.VARIANTS_GFF, r=ref, j=j)
log.info(cmd)
rcode = run_backticks(cmd)
self.assertEquals(0, rcode)
self.assertTrue(os.path.exists(os.path.join(self._output_dir, j)))
def _run_cmd(self, file_name):
"""Run an subprocess of the command and verify that report is present"""
exe = "ccs_report"
output_dir = tempfile.mkdtemp()
temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
json_report_file_name = temp_file.name
temp_file.close()
cmd = "{e} --debug --output-dir {o} {i} {r}".format(
e=exe, i=file_name, r=json_report_file_name, o=output_dir)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
with open(json_report_file_name, 'r') as f:
s = json.load(f)
log.info("JsonReport: ")
log.info(pprint.pformat(s, indent=4))
self.assertIsNotNone(s)
# cleanup
os.remove(json_report_file_name)
def _run_cmd(self, file_name):
"""Run an subprocess of the command and verify that report is present"""
exe = "ccs_report"
output_dir = tempfile.mkdtemp()
temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
json_report_file_name = temp_file.name
temp_file.close()
cmd = "{e} --debug --output-dir {o} {i} {r}".format(
e=exe,
i=file_name,
r=json_report_file_name,
o=output_dir)
rcode = run_backticks(cmd)
self.assertEqual(0, rcode)
with open(json_report_file_name, 'r') as f:
s = json.load(f)
log.info("JsonReport: ")
log.info(pprint.pformat(s, indent=4))
self.assertIsNotNone(s)
# cleanup
os.remove(json_report_file_name)
def test_basic(self):
output_dir = tempfile.mkdtemp(suffix="filter_stats_integration_")
t = tempfile.NamedTemporaryFile(dir=output_dir, delete=False)
t.close()
report_json = t.name
exe = "filter_stats"
cmd = "{e} --debug -o {o} -r {r} {csv}".format(e=exe, o=output_dir,
r=report_json,
csv=self.CSV_FILE)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
with open(report_json, 'r') as f:
s = json.load(f)
log.info("JsonReport: ")
log.info(pprint.pformat(s, indent=4))
self.assertIsNotNone(s)
# cleanup
os.remove(report_json)
def test_basic(self):
cmd = "overview_report --debug {i} {o}".format(i=self.input_file,
o=self.report_json)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
def test_help(self):
rcode = run_backticks("{e} --help".format(e=_EXE))
self.assertEqual(rcode, 0)
def test_basic(self):
csv = _generate_tmp_file()
cmd = _to_cmd(_INPUT_FOFN, _CONTROL_CMP_H5, csv)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
def test_help(self):
rcode = run_backticks("{e} --help".format(e=_EXE))
self.assertEqual(rcode, 0)
def test_basic(self):
csv = _generate_tmp_file()
cmd = _to_cmd(_INPUT_FOFN, _CONTROL_CMP_H5, csv)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)
def test_basic(self):
cmd = "overview_report --debug {i} {o}".format(i=self.input_file,
o=self.report_json)
rcode = run_backticks(cmd)
self.assertEqual(rcode, 0)