Python AlignmentSet.toExternalFiles方法代码示例

本文整理汇总了Python中pbcore.io.AlignmentSet.toExternalFiles方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentSet.toExternalFiles方法的具体用法？Python AlignmentSet.toExternalFiles怎么用？Python AlignmentSet.toExternalFiles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.toExternalFiles方法的5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_alignmentset_partial_consolidate

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import toExternalFiles [as 别名]
    def test_alignmentset_partial_consolidate(self):
        testFile = ("/mnt/secondary-siv/testdata/SA3-DS/"
                    "lambda/2372215/0007_tiny/Alignment_"
                    "Results/m150404_101626_42267_c10080"
                    "7920800000001823174110291514_s1_p0."
                    "all.alignmentset.xml")
        aln = AlignmentSet(testFile)
        nonCons= AlignmentSet(testFile)
        self.assertEqual(len(aln.toExternalFiles()), 3)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn, numFiles=2)
        self.assertFalse(os.path.exists(outfn))
        self.assertTrue(os.path.exists(_infixFname(outfn, "0")))
        self.assertTrue(os.path.exists(_infixFname(outfn, "1")))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        self.assertEqual(len(nonCons.toExternalFiles()), 3)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(nonCons))

        log.debug("Test cli")
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        datafile = os.path.join(outdir, "merged.bam")
        xmlfile = os.path.join(outdir, "merged.xml")
        cmd = "dataset.py consolidate --numFiles 2 {i} {d} {x}".format(
            i=testFile, d=datafile, x=xmlfile)
        log.debug(cmd)
        o, r, m = backticks(cmd)
        self.assertEqual(r, 0)

开发者ID:dyermd，项目名称:pbcore，代码行数:32，代码来源:test_pbdataset_subtypes.py

示例2: test_pbmerge_indexing

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import toExternalFiles [as 别名]
 def test_pbmerge_indexing(self):
     log.debug("Test through API")
     aln = AlignmentSet(data.getXml(12))
     self.assertEqual(len(aln.toExternalFiles()), 2)
     outdir = tempfile.mkdtemp(suffix="dataset-unittest")
     outfn = os.path.join(outdir, 'merged.bam')
     log.info(outfn)
     consolidateXml(aln, outfn, cleanup=False)
     self.assertTrue(os.path.exists(outfn))
     self.assertTrue(os.path.exists(outfn + '.pbi'))
     cons = AlignmentSet(outfn)
     self.assertEqual(len(aln), len(cons))
     orig_stats = os.stat(outfn + '.pbi')
     cons.externalResources[0].pbi = None
     self.assertEqual(None, cons.externalResources[0].pbi)
     # test is too quick, stat times might be within the same second
     time.sleep(1)
     cons.induceIndices()
     self.assertEqual(outfn + '.pbi', cons.externalResources[0].pbi)
     self.assertEqual(orig_stats, os.stat(cons.externalResources[0].pbi))
     cons.externalResources[0].pbi = None
     self.assertEqual(None, cons.externalResources[0].pbi)
     # test is too quick, stat times might be within the same second
     time.sleep(1)
     cons.induceIndices(force=True)
     self.assertNotEqual(orig_stats, os.stat(cons.externalResources[0].pbi))

开发者ID:PacificBiosciences，项目名称:pbcore，代码行数:28，代码来源:test_pbdataset_subtypes.py

示例3: test_alignmentset_partial_consolidate

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import toExternalFiles [as 别名]
 def test_alignmentset_partial_consolidate(self):
     testFile = ("/pbi/dept/secondary/siv/testdata/SA3-DS/"
                 "lambda/2372215/0007_tiny/Alignment_"
                 "Results/m150404_101626_42267_c10080"
                 "7920800000001823174110291514_s1_p0."
                 "all.alignmentset.xml")
     aln = AlignmentSet(testFile)
     nonCons = AlignmentSet(testFile)
     self.assertEqual(len(aln.toExternalFiles()), 3)
     outdir = tempfile.mkdtemp(suffix="dataset-unittest")
     outfn = os.path.join(outdir, 'merged.bam')
     aln.consolidate(outfn, numFiles=2)
     self.assertFalse(os.path.exists(outfn))
     self.assertTrue(os.path.exists(_infixFname(outfn, "0")))
     self.assertTrue(os.path.exists(_infixFname(outfn, "1")))
     self.assertEqual(len(aln.toExternalFiles()), 2)
     self.assertEqual(len(nonCons.toExternalFiles()), 3)
     for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
         self.assertEqual(read1, read2)
     self.assertEqual(len(aln), len(nonCons))

开发者ID:vrainish-pacbio，项目名称:pbcore，代码行数:22，代码来源:test_pbdataset_subtypes.py

示例4: test_alignmentset_consolidate

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import toExternalFiles [as 别名]
    def test_alignmentset_consolidate(self):
        log.debug("Test methods directly")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln,
                        useTmp=False)
        self.assertTrue(os.path.exists(outfn))
        consAln = AlignmentSet(outfn)
        self.assertEqual(len(consAln.toExternalFiles()), 1)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(consAln))

        log.debug("Test methods directly in tmp")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln,
                        useTmp=True)
        self.assertTrue(os.path.exists(outfn))
        consAln = AlignmentSet(outfn)
        self.assertEqual(len(consAln.toExternalFiles()), 1)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(consAln))

        log.debug("Test through API")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(nonCons))

        # Test that it is a valid xml:
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        datafile = os.path.join(outdir, "apimerged.bam")
        xmlfile = os.path.join(outdir, "apimerged.xml")
        log.debug(xmlfile)
        aln.write(xmlfile)

        log.debug("Test with cheap filter")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
        self.assertEqual(len(list(aln)), 7)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(list(aln)), len(list(nonCons)))

        log.debug("Test with not refname filter")
        # This isn't trivial with bamtools
        """
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
        self.assertEqual(len(list(aln)), 7)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(list(aln)), len(list(nonCons)))
        """

        log.debug("Test with expensive filter")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(accuracy=[('>', '.85')])
        self.assertEqual(len(list(aln)), 174)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
#.........这里部分代码省略.........

开发者ID:vrainish-pacbio，项目名称:pbcore，代码行数:103，代码来源:test_pbdataset_subtypes.py

示例5: test_alignmentset_consolidate

# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import toExternalFiles [as 别名]
    def test_alignmentset_consolidate(self):
        log.debug("Test methods directly")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln)
        self.assertTrue(os.path.exists(outfn))
        consAln = AlignmentSet(outfn)
        self.assertEqual(len(consAln.toExternalFiles()), 1)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(consAln))

        log.debug("Test through API")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(aln), len(nonCons))

        log.debug("Test with cheap filter")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
        self.assertEqual(len(list(aln)), 7)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(list(aln)), len(list(nonCons)))

        log.debug("Test with not refname filter")
        # This isn't trivial with bamtools
        """
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
        self.assertEqual(len(list(aln)), 7)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(list(aln)), len(list(nonCons)))
        """

        log.debug("Test with expensive filter")
        aln = AlignmentSet(data.getXml(12))
        self.assertEqual(len(list(aln)), 177)
        aln.filters.addRequirement(accuracy=[('>', '.85')])
        self.assertEqual(len(list(aln)), 174)
        self.assertEqual(len(aln.toExternalFiles()), 2)
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        outfn = os.path.join(outdir, 'merged.bam')
        aln.consolidate(outfn)
        self.assertTrue(os.path.exists(outfn))
        self.assertEqual(len(aln.toExternalFiles()), 1)
        nonCons = AlignmentSet(data.getXml(12))
        nonCons.filters.addRequirement(accuracy=[('>', '.85')])
        self.assertEqual(len(nonCons.toExternalFiles()), 2)
        for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
            self.assertEqual(read1, read2)
        self.assertEqual(len(list(aln)), len(list(nonCons)))

        log.debug("Test cli")
        outdir = tempfile.mkdtemp(suffix="dataset-unittest")
        datafile = os.path.join(outdir, "merged.bam")
        xmlfile = os.path.join(outdir, "merged.xml")
        cmd = "dataset.py consolidate {i} {d} {x}".format(i=data.getXml(12),
                                                          d=datafile,
                                                          x=xmlfile)
        log.debug(cmd)
        o, r, m = backticks(cmd)
        self.assertEqual(r, 0)

开发者ID:dyermd，项目名称:pbcore，代码行数:97，代码来源:test_pbdataset_subtypes.py

注：本文中的pbcore.io.AlignmentSet.toExternalFiles方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。