def __init__(self, filename, mutation_data_factory=None, configFile='vcf.in.config', genomeBuild="hg19", other_options=None):
"""
:param filename:
:param configFile:
"""
super(VcfInputMutationCreator, self).__init__(filename, mutation_data_factory, configFile, genomeBuild, other_options)
self.filename = filename
self.build = genomeBuild
self.configFilename = configFile
try:
self.vcf_reader = vcf.Reader(filename=self.filename, strict_whitespace=True)
except AttributeError as ae:
error_msg = "Could not parse VCF: " + str(self.filename) + ". This often occurs due to a malformed VCF."
logging.error(error_msg)
raise OncotatorException(error_msg, str(ae.message), traceback.format_exc())
self.configTableBuilder = ConfigTableCreatorFactory.getConfigTableCreatorInstance("input_vcf")
self.isTagSplit = dict()
self.logger = logging.getLogger(__name__)
if other_options is None:
other_options = {}
self.collapse_filter_fields = other_options.get(OptionConstants.COLLAPSE_FILTER_COLS, False)
self._is_skipping_no_alts = other_options.get(InputMutationCreatorOptions.IS_SKIP_ALTS, False)
def __init__(self, filename, configFile="vcf.out.config", otherOptions=None):
"""
:param filename: output filename
:param configFile: output config file
"""
self._filename = filename
self._otherOpts = dict() if otherOptions is None else otherOptions
self.configFilename = configFile
self.logger = logging.getLogger(__name__)
self.config = oncotator.utils.ConfigUtils.ConfigUtils.createConfigParser(configFile, ignoreCase=False)
self.chromHashCodeTable = None # maps every chromosome in the mutations to a sortable integer
self.configTableBuilder = ConfigTableCreatorFactory.getConfigTableCreatorInstance("output_vcf")
self.delimiter = "\t"
self.lineterminator = "\n"
self.sampleNames = [] # all sample names in the mutations
self.chroms = [] # all chromosomes in the mutations
def __init__(self, filename, configFile="vcf.out.config", otherOptions=None):
"""
:param filename: output filename
:param configFile: output config file
"""
self._filename = filename
self._otherOpts = dict() if otherOptions is None else otherOptions
self.configFilename = configFile
self.logger = logging.getLogger(__name__)
self.config = oncotator.utils.ConfigUtils.ConfigUtils.createConfigParser(configFile, ignoreCase=False)
self.chromHashCodeTable = None # maps every chromosome in the mutations to a sortable integer
self.configTableBuilder = ConfigTableCreatorFactory.getConfigTableCreatorInstance("output_vcf")
self.delimiter = "\t"
self.lineterminator = "\n"
self.sampleNames = [] # all sample names in the mutations
self.chroms = [] # all chromosomes in the mutations
def __init__(self, filename, configFile='vcf.in.config', genomeBuild="hg19", other_options=None):
"""
:param filename:
:param configFile:
"""
self.filename = filename
self.build = genomeBuild
self.configFilename = configFile
self.vcf_reader = vcf.Reader(filename=self.filename, strict_whitespace=True)
self.configTableBuilder = ConfigTableCreatorFactory.getConfigTableCreatorInstance("input_vcf")
self.isTagSplit = dict()
self.logger = logging.getLogger(__name__)
if other_options is None:
other_options = {}
self._is_skipping_no_alts = other_options.get(InputMutationCreatorOptions.IS_SKIP_ALTS, False)
def __init__(self, filename, configFile='vcf.in.config', genomeBuild="hg19", other_options=None):
"""
:param filename:
:param configFile:
"""
self.filename = filename
self.build = genomeBuild
self.configFilename = configFile
self.vcf_reader = vcf.Reader(filename=self.filename, strict_whitespace=True)
self.configTableBuilder = ConfigTableCreatorFactory.getConfigTableCreatorInstance("input_vcf")
self.isTagSplit = dict()
self.logger = logging.getLogger(__name__)
if other_options is None:
other_options = {}
self._is_skipping_no_alts = other_options.get(InputMutationCreatorOptions.IS_SKIP_ALTS, False)
