def test_alignment_reference(self): rs1 = ReferenceSet(data.getXml(9)) fasta_res = rs1.externalResources[0] fasta_file = urlparse(fasta_res.resourceId).path ds1 = AlignmentSet(data.getXml(8), referenceFastaFname=rs1) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) ds1 = AlignmentSet(data.getXml(8), referenceFastaFname=fasta_file) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) ds1 = AlignmentSet(data.getXml(8)) ds1.addReference(fasta_file) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None)
def test_alignment_reference(self): rfn = data.getXml(9) rs1 = ReferenceSet(data.getXml(9)) fasta_res = rs1.externalResources[0] fasta_file = urlparse(fasta_res.resourceId).path ds1 = AlignmentSet(data.getXml(8), referenceFastaFname=rs1) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) self.assertEqual(ds1.externalResources[0].reference, fasta_file) self.assertEqual(ds1.resourceReaders()[0].referenceFasta.filename, fasta_file) ds1 = AlignmentSet(data.getXml(8), referenceFastaFname=fasta_file) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) self.assertEqual(ds1.externalResources[0].reference, fasta_file) self.assertEqual(ds1.resourceReaders()[0].referenceFasta.filename, fasta_file) ds1 = AlignmentSet(data.getXml(8)) ds1.addReference(fasta_file) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) self.assertEqual(ds1.externalResources[0].reference, fasta_file) self.assertEqual(ds1.resourceReaders()[0].referenceFasta.filename, fasta_file) fofn_out = tempfile.NamedTemporaryFile(suffix=".fofn").name log.debug(fofn_out) with open(fofn_out, 'w') as f: f.write(data.getXml(8)) f.write('\n') f.write(data.getXml(11)) f.write('\n') ds1 = AlignmentSet(fofn_out, referenceFastaFname=fasta_file) aln_ref = None for aln in ds1: aln_ref = aln.reference() break self.assertTrue(aln_ref is not None) self.assertEqual(ds1.externalResources[0].reference, fasta_file) self.assertEqual(ds1.resourceReaders()[0].referenceFasta.filename, fasta_file)
def test_loading_reference(self): log.info('Opening Reference') r = ReferenceSet(data.getRef()).toExternalFiles()[0] log.info('Done Opening Reference') log.info('Opening AlignmentSet') d = AlignmentSet(data.getBam(), referenceFastaFname=r) log.info('Done Opening AlignmentSet') bfile = openIndexedAlignmentFile(data.getBam(), referenceFastaFname=r) self.assertTrue(bfile.isReferenceLoaded) for res in d.resourceReaders(): self.assertTrue(res.isReferenceLoaded) aln = AlignmentSet(data.getBam()) aln.addReference(r) for res in aln.resourceReaders(): self.assertTrue(res.isReferenceLoaded)
def loadBam(filename, referenceFname): filename = os.path.abspath(os.path.expanduser(filename)) aln = AlignmentSet(filename) aln.addReference(referenceFname) return aln