本文整理汇总了Python中pbcore.io.AlignmentSet.write方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentSet.write方法的具体用法？Python AlignmentSet.write怎么用？Python AlignmentSet.write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.write方法的10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: _make_alignmentset
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def _make_alignmentset(file_name=None):
bam = pbcore.data.getBamAndCmpH5()[0]
ds = AlignmentSet(bam)
if file_name is None:
file_name = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
ds.write(file_name)
return file_name示例2: test_uuid
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def test_uuid(self):
ds = AlignmentSet()
old = ds.uuid
_ = ds.newUuid()
self.assertNotEqual(old, ds.uuid)
aln = AlignmentSet(data.getXml(no=8))
oldUuid = aln.uuid
outdir = tempfile.mkdtemp(suffix="dataset-doctest")
outXml = os.path.join(outdir, 'tempfile.xml')
aln.write(outXml)
aln = AlignmentSet(outXml)
self.assertEqual(aln.uuid, oldUuid)示例3: test_write
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def test_write(self):
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfile = os.path.join(outdir, 'tempfile.xml')
ds1 = AlignmentSet(data.getBam())
ds1.write(outfile)
log.debug('Validated file: {f}'.format(f=outfile))
validateFile(outfile)
ds2 = AlignmentSet(outfile)
self.assertTrue(ds1 == ds2)
# Should fail when strict:
ds3 = AlignmentSet(data.getBam())
ds3.write(outfile)示例4: test_membership_filter
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def test_membership_filter(self):
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)[:1]
aln.filters.addRequirement(zm=[('in', hns)])
self.assertEqual(len(list(aln)), 5)
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)
aln.filters.addRequirement(zm=[('in', hns)])
self.assertEqual(len(list(aln)), 177)
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)
hns = [n for _ in range(10000) for n in hns]
hns = np.array(hns)
aln.filters.addRequirement(zm=[('in', hns)])
self.assertEqual(len(list(aln)), 177)
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)[:1]
hns = list(hns)
aln.filters.addRequirement(zm=[('in', hns)])
self.assertEqual(len(list(aln)), 5)
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)[:1]
hns = set(hns)
aln.filters.addRequirement(zm=[('in', hns)])
self.assertEqual(len(list(aln)), 5)
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
qnames = [r.qName for r in aln[:10]]
aln.filters.addRequirement(qname=[('in', qnames)])
self.assertEqual(len(list(aln)), 10)
fn = tempfile.NamedTemporaryFile(suffix="alignmentset.xml").name
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
hns = np.unique(aln.index.holeNumber)[:1]
aln.filters.addRequirement(zm=[('in', hns)])
aln.write(fn)
aln.close()
aln2 = AlignmentSet(fn)
self.assertEqual(len(list(aln2)), 5)示例5: to_chunked_alignmentset_files
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def to_chunked_alignmentset_files(alignmentset_path, reference_path,
max_total_nchunks, chunk_key, dir_name,
base_name, ext):
dset = AlignmentSet(alignmentset_path, strict=True)
dset_chunks = dset.split(contigs=True, maxChunks=max_total_nchunks,
breakContigs=True)
# sanity checking
reference_set = ReferenceSet(reference_path, strict=True)
d = {}
for i, dset in enumerate(dset_chunks):
chunk_id = '_'.join([base_name, str(i)])
chunk_name = '.'.join([chunk_id, ext])
chunk_path = os.path.join(dir_name, chunk_name)
dset.write(chunk_path)
d[chunk_key] = os.path.abspath(chunk_path)
d['$chunk.reference_id'] = reference_path
c = PipelineChunk(chunk_id, **d)
yield c示例6: test_alignmentset_consolidate
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [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.........
示例7: setUpClass
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def setUpClass(cls):
ds = AlignmentSet(pbcore.data.getBamAndCmpH5()[0], strict=True)
cls.alignment_set_xml = tempfile.NamedTemporaryFile(
suffix=".alignmentset.xml").name
ds.write(cls.alignment_set_xml)示例8: _get_input_file
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def _get_input_file(cls):
ds_xml = tempfile.NamedTemporaryFile(
suffix=".alignmentset.xml").name
ds = AlignmentSet(cls.ALIGNMENTS, strict=True)
ds.write(ds_xml)
return ds_xml示例9: setUpClass
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def setUpClass(cls):
super(TestPbreportMappingStats, cls).setUpClass()
ds = AlignmentSet(pbcore.data.getBamAndCmpH5()[0], strict=True)
ds.write(cls.INPUT_FILES[0])示例10: test_alignmentset_consolidate
# 需要导入模块: from pbcore.io import AlignmentSet [as 别名]
# 或者: from pbcore.io.AlignmentSet import write [as 别名]
def test_alignmentset_consolidate(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')
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)
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 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)