def __init__(self, src_file, title='', version=None, use_binary=True, proteinPositionAnnotation="protein_change", gpColumnNames="gene,start_AA,end_AA"): # In this case, we want to initialize with the Datasource class super(GenericGenomicPositionDatasource, self).__init__(src_file, title=title, version=version) self.proteinPositionAnnotation = proteinPositionAnnotation self.proteinRegexp = re.compile("[A-Z\*a-z]*([0-9]+)") index_mode = 'gene_protein_pos' self.db_obj, self.output_headers = get_db_data(src_file, title, use_binary, index_mode, gpColumnNames)
def __init__(self, src_file, title='', version=None, use_binary=True, gpColumnNames="chr,start,end"): super(GenericGenomicPositionDatasource, self).__init__(src_file, title=title, version=version) index_mode = 'genomic_pos' self.db_obj, self.output_headers = get_db_data(src_file, title, use_binary, index_mode, gpColumnNames)
def __init__(self, src_file, title='', version=None, use_binary=True, proteinPositionAnnotation="protein_change", gpColumnNames="gene,start_AA,end_AA"): # In this case, we want to initialize with the Datasource class super(GenericGenomicPositionDatasource, self).__init__(src_file, title=title, version=version) self.proteinPositionAnnotation = proteinPositionAnnotation self.protein_regexp = re.compile("[A-Z\*a-z]*([0-9]+)") self.protein_regex_range = re.compile("[A-Z\*a-z]*([0-9]+)_([0-9]+)") index_mode = 'gene_protein_pos' self.db_obj, self.output_headers = get_db_data(src_file, title, use_binary, index_mode, gpColumnNames)
def __init__(self, src_file, title='', version=None, use_binary=True, geneColumnName='gene'): super(GenericGeneDatasource, self).__init__(src_file, title=title, version=version) index_mode = 'gene' self.db_obj, self.output_headers = get_db_data(src_file, title, use_binary, index_mode,indexColumnNames=geneColumnName)