def __iter__(self):
brShelve1 = self._getBoundingRegionShelve(self._trackName1)
brShelve2 = self._getBoundingRegionShelve(self._trackName2)
allBrsAreWholeChrs1 = self._commonAllBoundingRegionsAreWholeChr(brShelve1) \
if brShelve1 is not None else False
allBrsAreWholeChrs2 = self._commonAllBoundingRegionsAreWholeChr(brShelve2) \
if brShelve2 is not None else False
for chr in GenomeInfo.getExtendedChrList(self.genome):
if brShelve1 is None:
yield GenomeRegion(self.genome, chr, 0, GenomeInfo.getChrLen(self.genome, chr))
else:
brList1 = brShelve1.getAllBoundingRegionsForChr(chr)
if brShelve2 is None or \
(allBrsAreWholeChrs2 and not allBrsAreWholeChrs1):
for reg in brList1:
yield reg
else:
brList2 = brShelve2.getAllBoundingRegionsForChr(chr)
if allBrsAreWholeChrs1 and not allBrsAreWholeChrs2:
for reg in brList2:
yield reg
else:
for reg in self.getAllIntersectingRegions(self.genome, chr, brList1, brList2):
yield reg
def getTotalBpSpan(self):
# print 'SELF: ', self.chr, self.start, self.end
if self.chr is None:
return sum(GenomeInfo.getChrLen(self.genome, chr) for chr in GenomeInfo.getExtendedChrList(self.genome))
# elif not self.start:
# return GenomeInfo.getChrLen(self.genome, self.chr)
else:
return len(self)
def getAllBoundingRegions(self):
if not self.fileExists():
from gtrackcore_memmap.util.CommonFunctions import prettyPrintTrackName
raise BoundingRegionsNotAvailableError('Bounding regions not available for track: ' + \
prettyPrintTrackName(self._trackName))
for chr in GenomeInfo.getExtendedChrList(self._genome):
for reg in self.getAllBoundingRegionsForChr(chr):
yield reg
def _removeBoundingRegionTuplesIfFullChrsAndNotFixedGapSize(self):
if self.getFixedGapSize() == 0 and not self._reprIsDense:
# If only full chromosomes
if all(
brt.region.chr in GenomeInfo.getExtendedChrList(self._genome)
and brt.region.start == 0
and brt.region.end == GenomeInfo.getChrLen(self._genome, brt.region.chr)
for brt in self._boundingRegionTuples
):
self._boundingRegionTuples = []
def parseRegSpec(regSpec, genome = None, includeExtraChrs = False):
from gtrackcore_memmap.track.core.GenomeRegion import GenomeRegion
from gtrackcore_memmap.metadata.GenomeInfo import GenomeInfo
class SimpleUserBinSource(list):
pass
regions = []
allRegSpecs = regSpec.strip().split(',')
for curRegSpec in allRegSpecs:
regParts = curRegSpec.strip().split(':')
if genome == None:
genome = regParts[0]
#assert GenomeInfo(genome).isInstalled(), "Specified genome is not installed: %s" % genome
if not (regParts[0]=='*' or regParts[0] in GenomeInfo.getExtendedChrList(genome)):
#if (regParts[0]=='*' or regParts[0].startswith('chr')):
# if genome == None:
# genome = DEFAULT_GENOME
#else:
# assert genome is None or genome == regParts[0], \
assert regParts[0] == genome, \
"Region specification does not start with one of '*' or correct chromosome or genome name. Region specification: %s. Genome: %s" % (curRegSpec, genome)
#genome = regParts[0]
regParts = regParts[1:]
if regParts[0] == '*':
assert len(regParts) == 1, \
"Region specification starts with '*' but continues with ':'. Region specification: %s" % curRegSpec
assert len(allRegSpecs) == 1, \
"Region specification is '*', but is in a list with other region specifications: %s" % regSpec
chrList = GenomeInfo.getExtendedChrList(genome) if includeExtraChrs else GenomeInfo.getChrList(genome)
for chr in chrList:
regions.append(GenomeRegion(genome, chr, 0, GenomeInfo.getChrLen(genome, chr)))
else:
#assert(regParts[0].startswith('chr')), \
assert regParts[0] in GenomeInfo.getExtendedChrList(genome), \
"Region specification does not start with chromosome specification. Region specification: %s " % curRegSpec
chr = regParts[0]
try:
chrLen = GenomeInfo.getChrLen(genome, chr)
except Exception, e:
raise InvalidFormatError("Chromosome '%s' does not exist for genome '%s'" % (chr, genome))
if len(regParts)>1:
posParts = regParts[1]
assert '-' in posParts, \
"Position specification does not include character '-'. Region specification: %s " % curRegSpec
rawStart, rawEnd = posParts.split('-')
start = int(rawStart.replace('k','001').replace('m','000001'))
end = int(rawEnd.replace('k','000').replace('m','000000')) if rawEnd != '' else chrLen
assert start >= 1, \
"Start position is not positive. Region specification: %s " % curRegSpec
assert end >= start, \
"End position is not larger than start position. Region specification: %s " % curRegSpec
assert end <= chrLen, \
"End position is larger than chromosome size. Genome: %s. Chromosome size: %s. Region specification: %s" % (genome, chrLen, curRegSpec)
#-1 for conversion from 1-indexing to 0-indexing end-exclusive
start-=1
else:
start,end = 0, chrLen
regions.append( GenomeRegion(genome, chr, start, end) )
def _isOldTypeChromDirectory(dirPath, genome):
if dirPath[-1] == os.sep:
dirPath = os.path.dirname(dirPath)
dirName = os.path.basename(dirPath)
return dirName in set(GenomeInfo.getExtendedChrList(genome)) and \
not any(os.path.isdir(os.path.join(dirPath, subFn)) for subFn in os.listdir(dirPath))
def _commonAllBoundingRegionsAreWholeChr(self, brShelve):
for chr in GenomeInfo.getExtendedChrList(self.genome):
for reg in brShelve.getAllBoundingRegionsForChr(chr):
if not reg.isWholeChr():
return False
return True
def getTotalElementCount(self):
return sum(self.getTotalElementCountForChr(chr) for chr in GenomeInfo.getExtendedChrList(self._genome))
