class GenePredTbl(list):
"""Table of GenePred objects loaded from a tab-file"""
def __init__(self, fileName, buildIdx=False, buildUniqIdx=False, buildRangeIdx=False):
if buildIdx and buildUniqIdx:
raise PycbioException("can't specify both buildIdx and buildUniqIdx")
for row in GenePredReader(fileName):
self.append(row)
self.names = None
self.rangeMap = None
if buildUniqIdx:
self._buildUniqIdx()
if buildIdx:
self._buildIdx()
if buildRangeIdx:
self._buildRangeIdx()
def _buildUniqIdx(self):
self.names = dict()
for row in self:
if row.name in self.names:
raise PycbioException("gene with this name already in index: " + row.name)
self.names[row.name] = row
def _buildIdx(self):
self.names = defaultdict(list)
for row in self:
self.names.append(row.name, row)
def _buildRangeIdx(self):
from pycbio.hgdata.RangeFinder import RangeFinder
self.rangeMap = RangeFinder()
for gene in self:
self.rangeMap.add(gene.chrom, gene.txStart, gene.txEnd, gene, gene.strand)
class GenePredTbl(list):
"""Table of GenePred objects loaded from a tab-file"""
def __init__(self, fileName, buildIdx=False, buildUniqIdx=False, buildRangeIdx=False):
if buildIdx and buildUniqIdx:
raise Exception("can't specify both buildIdx and buildUniqIdx")
for row in GenePredReader(fileName):
self.append(row)
self.names = None
self.rangeMap = None
if buildUniqIdx:
self.__buildUniqIdx()
if buildIdx:
self.__buildIdx()
if buildRangeIdx:
self.__buildRangeIdx()
def __buildUniqIdx(self):
self.names = dict()
for row in self:
if row.name in self.names:
raise Exception("gene with this name already in index: " + row.name)
self.names[row.name] = row
def __buildIdx(self):
from pycbio.sys.MultiDict import MultiDict
self.names = MultiDict()
for row in self:
self.names.add(row.name, row)
def __buildRangeIdx(self):
from pycbio.hgdata.RangeFinder import RangeFinder
self.rangeMap = RangeFinder()
for gene in self:
self.rangeMap.add(gene.chrom, gene.txStart, gene.txEnd, gene, gene.strand)
def __buildRangeIdx(self):
from pycbio.hgdata.RangeFinder import RangeFinder
self.rangeMap = RangeFinder()
for gene in self:
self.rangeMap.add(gene.chrom, gene.txStart, gene.txEnd, gene,
gene.strand)
def __buildRangeIdx(self):
from pycbio.hgdata.RangeFinder import RangeFinder
self.rangeMap = RangeFinder()
for gene in self:
self.rangeMap.add(gene.chrom, gene.txStart, gene.txEnd, gene, gene.strand)
