def test_addFilters(self):
ds1 = DataSet()
filt = Filters()
filt.addRequirement(rq=[('>', '0.85')])
ds1.addFilters(filt)
self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
# Or added from a source XML
ds2 = DataSet(data.getXml(16))
self.assertTrue(str(ds2.filters).startswith('( rname = E.faecalis'))
def test_addFilters(self):
ds1 = DataSet()
filt = Filters()
filt.addRequirement(rq=[('>', '0.85')])
ds1.addFilters(filt)
assert str(ds1.filters) == '( rq > 0.85 )'
# Or added from a source XML
ds2 = DataSet(data.getXml(15))
assert str(ds2.filters).startswith('( rname = E.faecalis')
def test_setFilters(self):
ds1 = DataSet()
filt = Filters()
filt.addRequirement(rq=[('>', '0.85')])
ds1.addFilters(filt)
self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
# Or added from a source XML
ds2 = DataSet()
ds2.filters = ds1.filters
self.assertEquals(str(ds2.filters), '( rq > 0.85 )')
def test_addFilters(self):
ds1 = DataSet()
filt = Filters()
filt.addRequirement(rq=[('>', '0.85')])
ds1.addFilters(filt)
self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
# Or added from a source XML
ds2 = DataSet(data.getXml(16))
self.assertTrue(str(ds2.filters).startswith(
'( rname = E.faecalis'))
def test_setFilters(self):
ds1 = DataSet()
filt = Filters()
filt.addRequirement(rq=[('>', '0.85')])
ds1.addFilters(filt)
self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
# Or added from a source XML
ds2 = DataSet()
ds2.filters = ds1.filters
self.assertEquals(str(ds2.filters), '( rq > 0.85 )')
def filterXml(args):
log.error("Adding filters via CLI is temporarily out of order")
exit(1)
if args.infile.endswith('xml'):
dataSet = DataSet(args.infile, strict=args.strict)
filters = []
separators = ['<=', '>=', '!=', '==', '>', '<', '=']
for filt in args.filters:
for sep in separators:
if sep in filt:
param, condition = filt.split(sep)
condition = sep + condition
filters[param] = condition
break
dataSet.addFilters([filters])
log.info("{i} filters added".format(i=len(filters)))
dataSet.write(args.outfile)
else:
raise IOError("No files found/found to be compatible")
def filterXml(args):
log.error("Adding filters via CLI is temporarily out of order")
exit(1)
if args.infile.endswith('xml'):
dataSet = DataSet(args.infile, strict=args.strict)
filters = []
separators = ['<=', '>=', '!=', '==', '>', '<', '=']
for filt in args.filters:
for sep in separators:
if sep in filt:
param, condition = filt.split(sep)
condition = sep + condition
filters[param] = condition
break
dataSet.addFilters([filters])
log.info("{i} filters added".format(i=len(filters)))
dataSet.write(args.outfile)
else:
raise IOError("No files found/found to be compatible")
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)
