本文整理汇总了Python中oncotator.utils.MutUtils.MutUtils.retrieveMutCoordinatesForRendering方法的典型用法代码示例。如果您正苦于以下问题：Python MutUtils.retrieveMutCoordinatesForRendering方法的具体用法？Python MutUtils.retrieveMutCoordinatesForRendering怎么用？Python MutUtils.retrieveMutCoordinatesForRendering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oncotator.utils.MutUtils.MutUtils的用法示例。
在下文中一共展示了MutUtils.retrieveMutCoordinatesForRendering方法的2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: _writeMuts2Tsv
# 需要导入模块: from oncotator.utils.MutUtils import MutUtils [as 别名]
# 或者: from oncotator.utils.MutUtils.MutUtils import retrieveMutCoordinatesForRendering [as 别名]
def _writeMuts2Tsv(self, muts, path):
"""
Given a mutation generator, this methods writes a tab separated file for all mutations in the mutation
generator. In addition, this method computes the appropriate sample name in scenarios where the mutation is
missing sample name annotation. It also computes a list of all chromosomes and sample names contained within
the generator.
:param path: temporary filename
:param muts: generator object with mutations
"""
sampleNames = set()
chroms = set()
writer = None
# create a temporary file to write tab-separated file
tempTsvFile = tempfile.NamedTemporaryFile(dir=path, delete=False)
self.logger.debug("Creating intermediate tsv file at %s" % tempTsvFile.name)
mutAttributeNames = []
sampleNameSelector = SampleNameSelector(self.mutation,
configFile=self.configTable.getConfigFilename(),
section="OTHER")
with open(tempTsvFile.name, 'w') as fptr:
ctr = 0
sampleNameAnnotationName = sampleNameSelector.getOutputAnnotationName()
sampleNameSource = sampleNameSelector.getAnnotationSource()
for mut in muts:
if len(mutAttributeNames) == 0:
mutAttributeNames = mut.getAttributeNames()
sampleName = sampleNameSelector.getSampleName(mut)
if sampleName is not None:
if mut.get(sampleNameAnnotationName, None) is None:
mut.createAnnotation(sampleNameAnnotationName, sampleName, sampleNameSource)
sampleNames.add(sampleName)
# Parse chromosome
chroms.add(mut.chr)
updated_start, updated_ref_allele, updated_alt_allele = MutUtils.retrieveMutCoordinatesForRendering(mut)
mut.ref_allele = updated_ref_allele
mut.alt_allele = updated_alt_allele
mut.start = updated_start
if ctr == 0:
fieldnames2Render = MutUtils.getAllAttributeNames(mut)
if sampleNameAnnotationName is not None:
fieldnames2Render += [sampleNameAnnotationName]
for fieldname in fieldnames2Render: # fieldnames that start "_" aren't rendered
if fieldname.startswith("_"):
fieldnames2Render.remove(fieldname)
writer = csv.DictWriter(fptr, fieldnames2Render, extrasaction='ignore', delimiter=self.delimiter,
lineterminator=self.lineterminator)
writer.writeheader()
writer.writerow(mut)
ctr += 1
if (ctr % 1000) == 0:
self.logger.info("Wrote " + str(ctr) + " mutations to tsv.")
sampleNames = list(sampleNames)
sampleNames.sort()
chroms = list(chroms)
return chroms, sampleNames, tempTsvFile.name示例2: _writeMuts2Tsv
# 需要导入模块: from oncotator.utils.MutUtils import MutUtils [as 别名]
# 或者: from oncotator.utils.MutUtils.MutUtils import retrieveMutCoordinatesForRendering [as 别名]
def _writeMuts2Tsv(self, muts, path):
"""
Given a mutation generator, this methods writes a tab separated file for all mutations in the mutation
generator. In addition, this method computes the appropriate sample name in scenarios where the mutation is
missing sample name annotation. It also computes a list of all chromosomes and sample names contained within
the generator.
:param filename: temporary filename
:param muts: generator object with mutations
"""
sampleNames = set()
chroms = set()
writer = None
# create a temporary file to write tab-separated file
tempTsvFile = tempfile.NamedTemporaryFile(dir=path, delete=False)
self.logger.info("Creating intermediate tsv file...")
sampleNameAnnotationNames = self.getAnnotationNames("SAMPLE_NAME")
tumorSampleNameAnnotationNames = self.getAnnotationNames("SAMPLE_TUMOR_NAME")
normalSampleNameAnnotationNames = self.getAnnotationNames("SAMPLE_NORMAL_NAME")
mutAttributeNames = []
with open(tempTsvFile.name, 'w') as fptr:
ctr = 0
for mut in muts:
sampleName = None
sampleNameAnnotationName = None
if len(mutAttributeNames) == 0:
mutAttributeNames = mut.getAttributeNames()
# Sample name annotation is present
if len(sampleNameAnnotationNames) != 0:
sampleNameAnnotationName = sampleNameAnnotationNames[0]
sampleName = mut[sampleNameAnnotationName]
# Both, tumor and normal sample name annotations are present
elif len(tumorSampleNameAnnotationNames) != 0 and len(normalSampleNameAnnotationNames) != 0:
tumorSampleNameAnnotationName = tumorSampleNameAnnotationNames[0]
normalSampleNameAnnotationName = normalSampleNameAnnotationNames[0]
sampleName = string.join([mut[normalSampleNameAnnotationName],
mut[tumorSampleNameAnnotationName]], sep="-")
sampleNameAnnotationName = MutUtils.SAMPLE_NAME_ANNOTATION_NAME
mut.createAnnotation(sampleNameAnnotationName, sampleName, "OUTPUT")
if ctr == 0:
self.logger.info("Sample name is the concatenation of %s and %s columns."
% (normalSampleNameAnnotationName, tumorSampleNameAnnotationName))
# Only tumor sample name is present
elif len(tumorSampleNameAnnotationNames) != 0:
tumorSampleNameAnnotationName = tumorSampleNameAnnotationNames[0]
sampleName = mut[tumorSampleNameAnnotationName]
sampleNameAnnotationName = MutUtils.SAMPLE_NAME_ANNOTATION_NAME
mut.createAnnotation(sampleNameAnnotationName, sampleName, "INPUT")
if ctr == 0:
self.logger.info("Sample name is %s column." % tumorSampleNameAnnotationName)
# Only normal sample name is present
elif len(normalSampleNameAnnotationNames) != 0:
normalSampleNameAnnotationName = normalSampleNameAnnotationNames[0]
sampleName = mut[normalSampleNameAnnotationName]
sampleNameAnnotationName = MutUtils.SAMPLE_NAME_ANNOTATION_NAME
mut.createAnnotation(sampleNameAnnotationName, sampleName, "INPUT")
if ctr == 0:
self.logger.info("Sample name is %s column." % normalSampleNameAnnotationName)
if sampleName is not None:
sampleNames.add(sampleName)
# Parse chromosome
chroms.add(mut.chr)
updated_start, updated_ref_allele, updated_alt_allele = MutUtils.retrieveMutCoordinatesForRendering(mut)
mut.ref_allele = updated_ref_allele
mut.alt_allele = updated_alt_allele
mut.start = updated_start
if ctr == 0:
fieldnames2Render = MutUtils.getAllAttributeNames(mut)
if sampleNameAnnotationName is not None:
fieldnames2Render += [sampleNameAnnotationName]
for fieldname in fieldnames2Render: # fieldnames that start "_" aren't rendered
if fieldname.startswith("_"):
fieldnames2Render.remove(fieldname)
writer = csv.DictWriter(fptr, fieldnames2Render, extrasaction='ignore', delimiter=self.delimiter,
lineterminator=self.lineterminator)
writer.writeheader()
writer.writerow(mut)
ctr += 1
if (ctr % 1000) == 0:
self.logger.info("Wrote " + str(ctr) + " mutations to tsv.")
sampleNames = list(sampleNames)
sampleNames.sort()
chroms = list(chroms)
#.........这里部分代码省略.........