Lines Matching refs:NGS
2 from ngs import NGS
16 run = NGS.openReadCollection(PrimaryOnly)
20 run = NGS.openReadCollection(PrimaryOnly)
24 run = NGS.openReadCollection(WithSecondary)
28 return NGS.openReadCollection(PrimaryOnly).getReference("supercont2.1")
31 return NGS.openReferenceSequence("NC_011752.1")
39 run = NGS.openReadCollection(PrimaryOnly)
43 run = NGS.openReadCollection("SRRsomejunk")
49 self.assertEqual(PrimaryOnly, NGS.openReadCollection(PrimaryOnly).getName())
52 gr = NGS.openReadCollection(PrimaryOnly).getReadGroup("C1ELY.6")
55 it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
58 it = NGS.openReadCollection(PrimaryOnly).getReferences()
61 ref = NGS.openReadCollection(PrimaryOnly).getReference("supercont2.1")
64 assert ( NGS.openReadCollection(PrimaryOnly).hasReference("supercont2.1") )
65 assert ( not NGS.openReadCollection(PrimaryOnly).hasReference("non-existent acc") )
68 al = NGS.openReadCollection(PrimaryOnly).getAlignment(PrimaryOnly + ".PA.1")
71 alIt = NGS.openReadCollection(PrimaryOnly).getAlignments(Alignment.primaryAlignment)
74 alIt = NGS.openReadCollection(PrimaryOnly).getAlignments(Alignment.secondaryAlignment)
77 alIt = NGS.openReadCollection(PrimaryOnly).getAlignments(Alignment.all)
80 self.assertEqual(3987701, NGS.openReadCollection(PrimaryOnly).getAlignmentCount())
83 …self.assertEqual(3987701, NGS.openReadCollection(PrimaryOnly).getAlignmentCount(Alignment.primaryA…
86 …self.assertEqual(0, NGS.openReadCollection(PrimaryOnly).getAlignmentCount(Alignment.secondaryAlign…
89 … self.assertEqual(3987701, NGS.openReadCollection(PrimaryOnly).getAlignmentCount(Alignment.all))
92 self.assertEqual(178, NGS.openReadCollection(WithSecondary).getAlignmentCount())
95 …self.assertEqual(168, NGS.openReadCollection(WithSecondary).getAlignmentCount(Alignment.primaryAli…
98 …self.assertEqual(10, NGS.openReadCollection(WithSecondary).getAlignmentCount(Alignment.secondaryAl…
101 … self.assertEqual(178, NGS.openReadCollection(WithSecondary).getAlignmentCount(Alignment.all))
105 alIt = NGS.openReadCollection(WithSecondary).getAlignmentRange(166, 5)
110 read = NGS.openReadCollection(PrimaryOnly).getRead(PrimaryOnly + ".R.1")
114 readIt = NGS.openReadCollection(PrimaryOnly).getReads(Read.all)
119 self.assertEqual(2280633, NGS.openReadCollection(PrimaryOnly).getReadCount())
122 readIt = NGS.openReadCollection(PrimaryOnly).getReadRange(2, 3)
139 read = NGS.openReadCollection(PrimaryOnly).getRead(PrimaryOnly + ".R.3")
317 readCollection = NGS.openReadCollection(PrimaryOnly)
329 readCollection = NGS.openReadCollection(SingleFragmentPerSpot)
360 …self.assertEqual("NC_000007.13", NGS.openReadCollection("SRR821492").getReference("chr7").getCanon…
366 self.assertTrue(NGS.openReadCollection("SRR821492").getReference("chrM").getIsCircular())
372 self.assertFalse(NGS.openReadCollection("SRR821492").getReference("chrM").getIsLocal())
402 it = NGS.openReadCollection(PrimaryOnly).getReferences()
410 it = NGS.openReadCollection(PrimaryOnly).getReferences()
416 …it = NGS.openReadCollection(WithSecondary).getReference("gi|169794206|ref|NC_010410.1|").getAlignm…
435 …it = NGS.openReadCollection(WithSecondary).getReference("gi|169794206|ref|NC_010410.1|").getAlignm…
447 …it = NGS.openReadCollection(WithSecondary).getReference("gi|169794206|ref|NC_010410.1|").getAlignm…
457 ref = NGS.openReadCollection(WithCircularRef).getReference("NC_012920.1")
470 gr = NGS.openReadCollection(PrimaryOnly).getReadGroup("C1ELY.6")
474 assert ( NGS.openReadCollection(PrimaryOnly).hasReadGroup("C1ELY.6") )
475 assert ( not NGS.openReadCollection(PrimaryOnly).hasReadGroup("non-existent read group") )
478 gr = NGS.openReadCollection(WithGroups).getReadGroup("GS57510-FS3-L03")
499 it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
507 it = NGS.openReadCollection(PrimaryOnly).getReadGroups();