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Python AlignmentSet.updateCounts方法代码示例

本文整理汇总了Python中pbcore.io.AlignmentSet.updateCounts方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentSet.updateCounts方法的具体用法？Python AlignmentSet.updateCounts怎么用？Python AlignmentSet.updateCounts使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pbcore.io.AlignmentSet的用法示例。


在下文中一共展示了AlignmentSet.updateCounts方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: test_len_h5

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
    def test_len_h5(self):
        # HdfSubreadSet
        # len means something else in bax/bas land. These numbers may actually
        # be correct...
        sset = HdfSubreadSet(data.getXml(17), strict=True)
        self.assertEqual(len(sset), 9)
        self.assertEqual(sset._length, (9, 128093))
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)

        # AlignmentSet with cmp.h5
        aln = AlignmentSet(upstreamData.getBamAndCmpH5()[1], strict=True)
        self.assertEqual(len(aln), 112)
        self.assertEqual(aln._length, (112, 59970))
        self.assertEqual(aln.totalLength, 59970)
        self.assertEqual(aln.numRecords, 112)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 59970)
        self.assertEqual(aln.numRecords, 112)
开发者ID:PacificBiosciences，项目名称:pbcore，代码行数:32，代码来源:test_pbdataset_subtypes.py

示例2: test_len

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
    def test_len(self):
        # AlignmentSet
        aln = AlignmentSet(data.getXml(8), strict=True)
        self.assertEqual(len(aln), 92)
        self.assertEqual(aln._length, (92, 123588))
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)
        self.assertEqual(sum(1 for _ in aln), 92)
        self.assertEqual(sum(len(rec) for rec in aln), 123588)

        # AlignmentSet with filters
        aln = AlignmentSet(data.getXml(15), strict=True)
        self.assertEqual(len(aln), 40)
        self.assertEqual(aln._length, (40, 52023))
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)

        # SubreadSet
        sset = SubreadSet(data.getXml(10), strict=True)
        self.assertEqual(len(sset), 92)
        self.assertEqual(sset._length, (92, 124093))
        self.assertEqual(sset.totalLength, 124093)
        self.assertEqual(sset.numRecords, 92)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 124093)
        self.assertEqual(sset.numRecords, 92)
        self.assertEqual(sum(1 for _ in sset), 92)
        self.assertEqual(sum(len(rec) for rec in sset), 124093)

        # ReferenceSet
        sset = ReferenceSet(data.getXml(9), strict=True)
        self.assertEqual(len(sset), 59)
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
开发者ID:PacificBiosciences，项目名称:pbcore，代码行数:61，代码来源:test_pbdataset_subtypes.py

示例3: test_updateCounts

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
    def test_updateCounts(self):
        log.info("Testing updateCounts without filters")
        aln = AlignmentSet(data.getBam(0))
        readers = aln.resourceReaders()

        expLen = 0
        for reader in readers:
            for record in reader:
                expLen += record.readLength
                self.assertEqual(
                    record.aStart, record.bam.pbi[record.rowNumber]['aStart'])
                self.assertEqual(
                    record.aEnd, record.bam.pbi[record.rowNumber]['aEnd'])

        expNum = 0
        for reader in readers:
            expNum += len(reader)

        accLen = aln.metadata.totalLength
        accNum = aln.metadata.numRecords

        self.assertEqual(expLen, accLen)
        self.assertEqual(expNum, accNum)

        log.info("Testing whether filters are respected")
        aln.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
        aln.updateCounts()
        accLen = aln.metadata.totalLength
        accNum = aln.metadata.numRecords

        def count(gen):
            count = 0
            for _ in gen:
                count += 1
            return count

        expLen = 0
        for reader in readers:
            for record in reader:
                expLen += record.readLength

        bfile = openIndexedAlignmentFile(data.getBam(0))
        rWin = (bfile.referenceInfo('E.faecalis.1').ID,
                0,
                bfile.referenceInfo('E.faecalis.1').Length)
        reads = bfile.readsInRange(*rWin)
        expNum = count(reads)
        expLen = 0
        reads = bfile.readsInRange(*rWin)
        for read in reads:
            expLen += read.readLength

        self.assertEqual(expLen, accLen)
        self.assertEqual(expNum, accNum)
开发者ID:jrharting，项目名称:pbcore，代码行数:56，代码来源:test_pbdataset.py

示例4: test_filter_cli

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
 def test_filter_cli(self):
     outdir = tempfile.mkdtemp(suffix="dataset-unittest")
     outfn = os.path.join(outdir, "filtered8.xml")
     log.debug(outfn)
     cmd = "dataset filter {i} {o} {f}".format(
         i=data.getXml(8),
         o=outfn,
         f="rname=E.faecalis.1")
     log.debug(cmd)
     o, r, m = backticks(cmd)
     if r != 0:
         log.debug(m)
     self.assertEqual(r, 0)
     self.assertTrue(os.path.exists(outfn))
     aln = AlignmentSet(data.getXml(8))
     aln.filters.addRequirement(rname=[('=', 'E.faecalis.1')])
     aln.updateCounts()
     dset = AlignmentSet(outfn)
     self.assertEqual(str(aln.filters), str(dset.filters))
     self.assertEqual(aln.totalLength, dset.totalLength)
     self.assertEqual(aln.numRecords, dset.numRecords)
开发者ID:WenchaoLin，项目名称:pbcoretools，代码行数:23，代码来源:test_pbdataset.py

示例5: test_len

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
    def test_len(self):
        # AlignmentSet
        aln = AlignmentSet(data.getXml(8), strict=True)
        self.assertEqual(len(aln), 92)
        self.assertEqual(aln._length, (92, 123588))
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)
        self.assertEqual(sum(1 for _ in aln), 92)
        self.assertEqual(sum(len(rec) for rec in aln), 123588)

        # AlignmentSet with filters
        aln = AlignmentSet(data.getXml(15), strict=True)
        self.assertEqual(len(aln), 40)
        self.assertEqual(aln._length, (40, 52023))
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)

        # AlignmentSet with cmp.h5
        aln = AlignmentSet(upstreamData.getBamAndCmpH5()[1], strict=True)
        self.assertEqual(len(aln), 112)
        self.assertEqual(aln._length, (112, 59970))
        self.assertEqual(aln.totalLength, 59970)
        self.assertEqual(aln.numRecords, 112)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 59970)
        self.assertEqual(aln.numRecords, 112)


        # SubreadSet
        sset = SubreadSet(data.getXml(10), strict=True)
        self.assertEqual(len(sset), 92)
        self.assertEqual(sset._length, (92, 124093))
        self.assertEqual(sset.totalLength, 124093)
        self.assertEqual(sset.numRecords, 92)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 124093)
        self.assertEqual(sset.numRecords, 92)
        self.assertEqual(sum(1 for _ in sset), 92)
        self.assertEqual(sum(len(rec) for rec in sset), 124093)

        # HdfSubreadSet
        # len means something else in bax/bas land. These numbers may actually
        # be correct...
        sset = HdfSubreadSet(data.getXml(17), strict=True)
        self.assertEqual(len(sset), 9)
        self.assertEqual(sset._length, (9, 128093))
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)

        # ReferenceSet
        sset = ReferenceSet(data.getXml(9), strict=True)
        self.assertEqual(len(sset), 59)
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
开发者ID:vrainish-pacbio，项目名称:pbcore，代码行数:92，代码来源:test_pbdataset_subtypes.py

示例6: test_len

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import updateCounts [as 别名]
    def test_len(self):
        # AlignmentSet
        aln = AlignmentSet(data.getXml(8), strict=True)
        self.assertEqual(len(aln), 92)
        self.assertEqual(aln._length, (92, 123588))
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 123588)
        self.assertEqual(aln.numRecords, 92)

        # AlignmentSet with filters
        aln = AlignmentSet(data.getXml(15), strict=True)
        self.assertEqual(len(aln), 40)
        self.assertEqual(aln._length, (40, 52023))
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)
        aln.totalLength = -1
        aln.numRecords = -1
        self.assertEqual(aln.totalLength, -1)
        self.assertEqual(aln.numRecords, -1)
        aln.updateCounts()
        self.assertEqual(aln.totalLength, 52023)
        self.assertEqual(aln.numRecords, 40)

        # NO LONGER SUPPORTED AlignmentSet with cmp.h5
        #aln = AlignmentSet(upstreamData.getCmpH5(), strict=True)
        #self.assertEqual(len(aln), 84)
        #self.assertEqual(aln._length, (84, 26103))
        #self.assertEqual(aln.totalLength, 26103)
        #self.assertEqual(aln.numRecords, 84)
        #aln.totalLength = -1
        #aln.numRecords = -1
        #self.assertEqual(aln.totalLength, -1)
        #self.assertEqual(aln.numRecords, -1)
        #aln.updateCounts()
        #self.assertEqual(aln.totalLength, 26103)
        #self.assertEqual(aln.numRecords, 84)


        # SubreadSet
        # TODO Turn this back on when pbi's are fixed for subreadsets
        #sset = SubreadSet(data.getXml(10), strict=True)
        #self.assertEqual(len(sset), 92)
        #self.assertEqual(sset._length, (92, 123588))
        #self.assertEqual(sset.totalLength, 123588)
        #self.assertEqual(sset.numRecords, 92)
        #sset.totalLength = -1
        #sset.numRecords = -1
        #self.assertEqual(sset.totalLength, -1)
        #self.assertEqual(sset.numRecords, -1)
        #sset.updateCounts()
        #self.assertEqual(sset.totalLength, 123588)
        #self.assertEqual(sset.numRecords, 92)

        # HdfSubreadSet
        # len means something else in bax/bas land. These numbers may actually
        # be correct...
        sset = HdfSubreadSet(data.getXml(17), strict=True)
        self.assertEqual(len(sset), 9)
        self.assertEqual(sset._length, (9, 128093))
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 128093)
        self.assertEqual(sset.numRecords, 9)

        # ReferenceSet
        sset = ReferenceSet(data.getXml(9), strict=True)
        self.assertEqual(len(sset), 59)
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
        sset.totalLength = -1
        sset.numRecords = -1
        self.assertEqual(sset.totalLength, -1)
        self.assertEqual(sset.numRecords, -1)
        sset.updateCounts()
        self.assertEqual(sset.totalLength, 85774)
        self.assertEqual(sset.numRecords, 59)
开发者ID:dyermd，项目名称:pbcore，代码行数:89，代码来源:test_pbdataset_subtypes.py


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