def _createChildren(self):
self._addChild(
PointCountInsideSegsStat(self._region, self._track, self._track2))
self._addChild(CountStat(self._region, self._track2))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=False, interval=True)))
def _createChildren(self):
self._bpCount = self._addChild( CountStat(self._region, self._track, **self._kwArgs))
self._globalCatBinSizes = self._addChild( SizePerCatOfCategoricBinsStat(self._globalSource, self._track, **self._kwArgs))
#self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(allowOverlaps=self._configuredToAllowOverlaps(strict=False))) )
pass
def _createChildren(self):
self._addChild(CountStat(self._region, self._track))
self._addChild(SumStat(self._region, self._track2))
self._addChild(SumInsideStat(self._region, self._track, self._track2))
self._addChild(SumOfSquaresStat(self._region, self._track2))
self._addChild(
SumOfSquaresInsideStat(self._region, self._track, self._track2))
self._addChild(BinSizeStat(self._region, self._track))
def _createChildren(self):
#self._track provide intervals for inside vs outside, self._track2 provide values
sumInsideStat = SumInsideStat(self._region, self._track, self._track2)
countInsideStat = CountStat(self._region, self._track)
#sumAllStat = SumStat(self._region, self._track2)
sumAllStat = SumOverCoveredBpsStat(self._region, self._track2)
countAllStat = CountStat(self._region, self._track2)
self._addChild(sumInsideStat)
self._addChild(countInsideStat)
self._addChild(sumAllStat)
self._addChild(countAllStat)
from config.Config import IS_EXPERIMENTAL_INSTALLATION
if not IS_EXPERIMENTAL_INSTALLATION:
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=True)))
def _createChildren(self):
#self._track: defines inside vs outside
#self._track2: provides values
self._addChild(
AggregateOfCoveredBpsInSegmentsStat(self._region,
self._track2,
self._track,
method='sum_of_sum'))
self._addChild(SumOverCoveredBpsStat(self._region, self._track2))
self._addChild(CountStat(self._region, self._track))
self._addChild(BinSizeStat(self._region, self._track))
self._addChild(RawOverlapStat(self._region, self._track, self._track2))
def _createChildren(self):
#countClass = CountPointAllowingOverlapStat if self._configuredToAllowOverlaps(strict=False) else CountPointStat
globCount1 = CountStat(self._globalSource, self._track, **self._kwArgs)
globCount2 = CountStat(self._globalSource, self._track2,
**self._kwArgs)
if self._kernelType == 'uniform':
binCountClass = CountStat
elif self._kernelType == 'binSizeNormalized':
binCountClass = ProportionCountPerBinAvgStat
elif self._kernelType == 'catCoverageNormalized':
binCountClass = CatCoverageNormalizedCountStat
else:
binCountClass = KernelWeightedCountStat
binCount1 = binCountClass(self._region, self._track, **self._kwArgs)
binCount2 = binCountClass(self._region, self._track2, **self._kwArgs)
self._addChild(globCount1)
self._addChild(globCount2)
self._addChild(binCount1)
self._addChild(binCount2)
def _createChildren(self):
self._sumOfSquares = self._addChild(
SumOfSquaresStat(self._region, self._track))
self._sum = self._addChild(SumStat(self._region, self._track))
self._count = self._addChild(CountStat(self._region, self._track))
def _createChildren(self):
self._addChild(SumStat(self._region, self._track))
self._addChild(CountStat(self._region, self._track))
from gold.track.Track import PlainTrack
from gold.track.GenomeRegion import GenomeRegion
from gold.statistic.CountStat import CountStat
#create a track
track = PlainTrack(['Genes and gene subsets', 'Genes', 'Refseq'])
#create a region of interest
region = GenomeRegion('hg18', 'chr1', 1000, 900000)
#create a statistic
stat = CountStat(region, track)
print stat.getResult()
#What happens now:
#CountStat inherits MagicStatFactory
#MagicStatFactory determines that region may be splitted to smaller bins and looks for a CountStatSplittable.
#CountStatSplittable exists, and is instantiated.
#getResults first calls createChildren. CountStatSplittable now creates a new CountStat for a smaller first region.
#This times, when MagicStatFactory handles CountStat-creation it sees that the region in question should not be splitted.
#MagicStatFactory thus instantiates a CountStatUnsplittable, which loads track data, and does the count for its small bin.
#This is repeated for each small bin, and results are collected by CountStatSplittable.
#Finally, the method combineResults (of CountStatSplittable) computes the total results for the queried region and returns this.
def _createChildren(self):
self._addChild(SumInsideStat(self._region, self._track, self._track2))
self._addChild(CountStat(self._region, self._track))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(interval=False, dense=False)))
def _createChildren(self):
self._addChild(SumAtPointsStat(self._region, self._track,
self._track2))
self._addChild(CountStat(self._region, self._track))
def _createChildren(self):
self._addChild(CountStat(self._region, self._track))
self._binSizeStat = self._addChild(
BinSizeStat(self._region, self._track))
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with The Genomic HyperBrowser. If not, see <http://www.gnu.org/licenses/>.
from gold.track.Track import PlainTrack
from gold.track.GenomeRegion import GenomeRegion
from gold.statistic.CountStat import CountStat
#create a track
track = PlainTrack(['Genes and gene subsets','Genes','Refseq'])
#create a region of interest
region = GenomeRegion('hg18','chr1',1000,900000)
#create a statistic
stat = CountStat(region, track)
print stat.getResult()
#What happens now:
#CountStat inherits MagicStatFactory
#MagicStatFactory determines that region may be splitted to smaller bins and looks for a CountStatSplittable.
#CountStatSplittable exists, and is instantiated.
#getResults first calls createChildren. CountStatSplittable now creates a new CountStat for a smaller first region.
#This times, when MagicStatFactory handles CountStat-creation it sees that the region in question should not be splitted.
#MagicStatFactory thus instantiates a CountStatUnsplittable, which loads track data, and does the count for its small bin.
#This is repeated for each small bin, and results are collected by CountStatSplittable.
#Finally, the method combineResults (of CountStatSplittable) computes the total results for the queried region and returns this.