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))