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):
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_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 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
