def test_reads_in_reference(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
# See test_ref_names for why this is expected:
rn = refNames[15]
reads = ds.readsInReference(rn)
self.assertEqual(len(list(reads)), 11)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
reads = ds2.readsInReference("E.faecalis.2")
self.assertEqual(len(list(reads)), 3)
ds2 = DataSet(data.getXml(8))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
ds2.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
# Because of the filter!
reads = ds2.readsInReference("E.faecalis.2")
self.assertEqual(len(list(reads)), 0)
def test_reads_in_reference(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
# See test_ref_names for why this is expected:
rn = refNames[15]
reads = ds.readsInReference(rn)
self.assertEqual(len(list(reads)), 11)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
reads = ds2.readsInReference("E.faecalis.2")
self.assertEqual(len(list(reads)), 3)
ds2 = DataSet(data.getXml(8))
reads = ds2.readsInReference("E.faecalis.1")
self.assertEqual(len(list(reads)), 20)
ds2.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
# Because of the filter!
reads = ds2.readsInReference("E.faecalis.2")
self.assertEqual(len(list(reads)), 0)
def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
def test_reads_in_contig(self):
log.info("Testing reads in contigs")
ds = DataSet(data.getXml(8))
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 12)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
ds = DataSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '100')])
ds.addFilters(filt)
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 12)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
ds = DataSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '1000')])
ds.addFilters(filt)
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 9)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 1)
def test_reads_in_contig(self):
log.info("Testing reads in contigs")
ds = DataSet(data.getXml(8))
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 12)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
ds = DataSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '100')])
ds.addFilters(filt)
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 12)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 3)
ds = DataSet(data.getXml(8))
filt = Filters()
filt.addRequirement(length=[('>', '1000')])
ds.addFilters(filt)
dss = ds.split(contigs=True)
self.assertEqual(len(dss), 9)
efaec1TimesFound = 0
efaec1TotFound = 0
efaec2TimesFound = 0
efaec2TotFound = 0
for ds in dss:
ef1 = len(list(ds.readsInReference('E.faecalis.1')))
ef2 = len(list(ds.readsInReference('E.faecalis.2')))
if ef1:
efaec1TimesFound += 1
efaec1TotFound += ef1
if ef2:
efaec2TimesFound += 1
efaec2TotFound += ef2
self.assertEqual(efaec1TimesFound, 1)
self.assertEqual(efaec1TotFound, 20)
self.assertEqual(efaec2TimesFound, 1)
self.assertEqual(efaec2TotFound, 1)