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)
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, 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)