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_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 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 test_filter_reference_contigs(self): ds2 = ReferenceSet(data.getRef()) self.assertEqual(len(list(ds2.refNames)), 59) filt = Filters() filt.addRequirement(id=[('==', 'E.faecalis.1')]) ds2.addFilters(filt) self.assertEqual(str(ds2.filters), "( id == E.faecalis.1 )") self.assertEqual(len(ds2.refNames), 1) self.assertEqual(len(list(ds2.records)), 1) ds2.disableFilters() self.assertEqual(len(list(ds2.refNames)), 59) self.assertEqual(len(list(ds2.records)), 59) ds2.enableFilters() self.assertEqual(len(list(ds2.refNames)), 1) self.assertEqual(len(list(ds2.records)), 1)
def test_filter_reference_contigs(self): ds2 = ReferenceSet(data.getRef()) self.assertEqual(len(list(ds2.refNames)), 59) filt = Filters() filt.addRequirement(id=[('==', 'E.faecalis.1')]) ds2.addFilters(filt) self.assertEqual(str(ds2.filters), "( id == E.faecalis.1 )") self.assertEqual(len(ds2.refNames), 1) self.assertEqual(len(list(ds2.records)), 1) ds2.disableFilters() self.assertEqual(len(list(ds2.refNames)), 59) self.assertEqual(len(list(ds2.records)), 59) ds2.enableFilters() self.assertEqual(len(list(ds2.refNames)), 1) self.assertEqual(len(list(ds2.records)), 1)
def test_filter_reference_contigs(self): ds2 = ReferenceSet(data.getRef()) assert len(list(ds2.refNames)) == 59 assert len(list(ds2.records)) == len(ds2.index) filt = Filters() filt.addRequirement(id=[('==', 'E.faecalis.1')]) ds2.addFilters(filt) assert str(ds2.filters) == "( id == E.faecalis.1 )" assert len(ds2.refNames) == 1 assert len(list(ds2.records)) == 1 assert len(list(ds2.records)) == len(ds2.index) ds2.disableFilters() assert len(list(ds2.refNames)) == 59 assert len(list(ds2.records)) == 59 assert len(list(ds2.records)) == len(ds2.index) ds2.enableFilters() assert len(list(ds2.refNames)) == 1 assert len(list(ds2.records)) == 1 assert len(list(ds2.records)) == len(ds2.index)
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)