def test_exit_code_0_referenceset(self):
"""
Like a cram test. Assert exits with 0 with ReferenceSet XML
"""
ref = os.path.join(self._data_dir, 'references', 'lambda', 'sequence',
'lambda.fasta')
ref_name = os.path.join(self._output_dir, "refset.xml")
refset = ReferenceSet(ref)
refset.write(ref_name)
ref = ref_name
gff = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
r = 'rpt.json'
cmd = 'python -m pbreports.report.coverage {o} {r} {c} {g}'.format(o=self._output_dir,
r=r,
c=ref, g=gff)
log.info(cmd)
o, c, m = backticks(cmd)
if c is not 0:
log.error(m)
log.error(o)
sys.stderr.write(str(m) + "\n")
self.assertEquals(0, c)
self.assertTrue(os.path.exists(os.path.join(self._output_dir, r)))
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_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_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 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.REFERENCE)
refset.write(ref_name)
ref = ref_name
r = op.join(self._output_dir, 'rpt.json')
cmd = 'python -m pbreports.report.coverage {c} {g} {r}'.format(
r=r, c=ref, g=self.GFF)
log.info(cmd)
o, c, m = backticks(cmd)
if c is not 0:
log.error(m)
log.error(o)
sys.stderr.write(str(m) + "\n")
self.assertEquals(0, c)
self.assertTrue(op.exists(r))
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.REFERENCE)
refset.write(ref_name)
ref = ref_name
r = op.join(self._output_dir, 'rpt.json')
cmd = 'python -m pbreports.report.coverage {c} {g} {r}'.format(
r=r, c=ref, g=self.GFF)
log.info(cmd)
o, c, m = backticks(cmd)
if c is not 0:
log.error(m)
log.error(o)
sys.stderr.write(str(m) + "\n")
self.assertEquals(0, c)
self.assertTrue(op.exists(r))
