def serializeAlleleCountDataTo(self, stream):
type = getStreamType(stream)
stream.opentag('allelecounts')
for locus in self.freqcount.keys():
stream.writeln()
stream.opentag('locus', name=locus)
stream.writeln()
stream.closetag('allelecounts')
return 1
def serializeAlleleCountDataTo(self, stream):
type = getStreamType(stream)
stream.opentag('allelecounts')
for locus in self.freqcount.keys():
stream.writeln()
stream.opentag('locus', name=locus)
stream.writeln()
stream.closetag('allelecounts')
return 1
def serializeMetadataTo(self, stream):
type = getStreamType(stream)
stream.opentag('populationdata')
stream.writeln()
if self.popData:
for summary in self.popData.keys():
# convert metadata name into a XML tag name
tagname = string.lower(string.replace(summary, ' ', '-'))
stream.tagContents(tagname, self.popData[summary])
stream.writeln()
# call subclass-specific metadata serialization
self.serializeSubclassMetadataTo(stream)
stream.closetag('populationdata')
stream.writeln()
def serializeMetadataTo(self, stream):
type = getStreamType(stream)
stream.opentag('populationdata')
stream.writeln()
if self.popData:
for summary in self.popData.keys():
# convert metadata name into a XML tag name
tagname = string.lower(string.replace(summary,' ','-'))
stream.tagContents(tagname, self.popData[summary])
stream.writeln()
# call subclass-specific metadata serialization
self.serializeSubclassMetadataTo(stream)
stream.closetag('populationdata')
stream.writeln()
def serializeHomozygosityTo(self, stream):
type = getStreamType(stream)
if self.expectedStatsFlag:
stream.opentag('homozygosity')
stream.writeln()
stream.tagContents('observed',
"%.4f" % self.getObservedHomozygosity())
stream.writeln()
stream.tagContents('expected',
"%.4f" % self.getExpectedHomozygosity())
stream.writeln()
stream.tagContents('normdev',
"%.4f" % self.getNormDevHomozygosity())
stream.writeln()
#stream.tagContents('expectedVariance', "%.4f" % self.getVarExpectedHomozygosity())
#stream.writeln()
#stream.tagContents('expectedStdErr', "%.4f" % self.getSemExpectedHomozygosity())
#stream.writeln()
stream.opentag('pvalue')
lb, up = self.getPValueRange()
stream.tagContents('lower', "%.4f" % lb)
stream.tagContents('upper', "%.4f" % up)
stream.closetag('pvalue')
stream.writeln()
stream.closetag('homozygosity')
elif self.sampleCount == 0:
stream.emptytag('homozygosity', role='no-data')
else:
stream.opentag('homozygosity', role='out-of-range')
stream.writeln()
stream.tagContents('observed',
"%.4f" % self.getObservedHomozygosity())
stream.writeln()
stream.closetag('homozygosity')
# always end on a newline
stream.writeln()
def serializeTo(self, stream, allelelump=0):
type = getStreamType(stream)
# stream serialization goes here
stream.opentag('hardyweinberg', allelelump=("%d" % allelelump))
stream.writeln()
stream.tagContents("samplesize", "%d" % self.n)
stream.writeln()
# don't print out, already printed out in <allelecounts> tag in ParseFile
# stream.tagContents("distinctalleles", "%d" % self.k)
# stream.writeln()
stream.tagContents("lumpBelow", "%d" % self.lumpBelow)
stream.writeln()
self.serializeXMLTableTo(stream)
if self.flagHoms == 1:
stream.opentag('homozygotes')
stream.writeln()
stream.tagContents("observed", "%d" % self.totalHomsObs)
stream.writeln()
stream.tagContents("expected", "%4f" % self.totalHomsExp)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.totalChisqHoms)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.chisqHomsPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('homozygotes')
stream.writeln()
if self.flagHets == 1:
stream.opentag('heterozygotes')
stream.writeln()
stream.tagContents("observed", "%d" % self.totalHetsObs)
stream.writeln()
stream.tagContents("expected", "%4f" % self.totalHetsExp)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.totalChisqHets)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.chisqHetsPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('heterozygotes')
stream.writeln()
# loop for heterozygotes by allele
stream.opentag('heterozygotesByAllele')
stream.writeln()
for allele in self.hetsChisqByAllele.keys():
stream.opentag('allele', name=allele)
stream.writeln()
stream.tagContents("observed", "%d" % self.hetsObservedByAllele[allele])
stream.writeln()
stream.tagContents("expected", "%4f" % self.hetsExpectedByAllele[allele])
stream.writeln()
stream.tagContents("chisq", "%4f" % self.hetsChisqByAllele[allele])
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.hetsPvalByAllele[allele])
stream.writeln()
stream.closetag('allele')
stream.writeln()
stream.closetag('heterozygotesByAllele')
stream.writeln()
if self.flagLumps == 1:
stream.opentag('lumped')
stream.writeln()
stream.tagContents("observed", "%d" % self.lumpedObservedGenotypes)
stream.writeln()
stream.tagContents("expected", "%4f" % self.lumpedExpectedGenotypes)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.lumpedChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.lumpedChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('lumped')
stream.writeln()
else:
if self.flagNoRareGenotypes == 1:
stream.emptytag('lumped', role='no-rare-genotypes')
elif self.flagTooFewExpected == 1:
stream.emptytag('lumped', role='too-few-expected')
else:
stream.emptytag('lumped', role='not-calculated')
if self.flagCommons == 1:
stream.opentag('common')
stream.writeln()
stream.tagContents("observed", "%d" % self.commonObservedAccumulator)
stream.writeln()
stream.tagContents("expected", "%4f" % self.commonExpectedAccumulator)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.HWChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.HWChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "%d" % int(self.HWChisqDf))
stream.writeln()
stream.closetag('common')
stream.writeln()
else:
if self.flagNoCommonGenotypes == 1:
stream.emptytag('common', role='no-common-genotypes')
elif self.flagTooManyParameters == 1:
stream.emptytag('common', role='too-many-parameters')
else:
stream.emptytag('common', role='not-calculated')
stream.writeln()
if self.flagCommonPlusLumped == 1:
stream.opentag('commonpluslumped')
stream.writeln()
stream.tagContents("observed", "%d" % self.commonPlusLumpedObserved)
stream.writeln()
stream.tagContents("expected", "%4f" % self.commonPlusLumpedExpected)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.commonPlusLumpedChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.commonPlusLumpedChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "%d" % int(self.commonPlusLumpedChisqDf))
stream.writeln()
stream.closetag('commonpluslumped')
stream.writeln()
else:
stream.emptytag('commonpluslumped', role='not-calculated')
stream.writeln()
stream.closetag('hardyweinberg')
# extra spacer line
stream.writeln()
def serializeTo(self, stream, allelelump=0):
type = getStreamType(stream)
# stream serialization goes here
stream.opentag('hardyweinberg', allelelump=("%d" % allelelump))
stream.writeln()
stream.tagContents("samplesize", "%d" % self.n)
stream.writeln()
# don't print out, already printed out in <allelecounts> tag in ParseFile
# stream.tagContents("distinctalleles", "%d" % self.k)
# stream.writeln()
stream.tagContents("lumpBelow", "%d" % self.lumpBelow)
stream.writeln()
self.serializeXMLTableTo(stream)
if self.flagHoms == 1:
stream.opentag('homozygotes')
stream.writeln()
stream.tagContents("observed", "%d" % self.totalHomsObs)
stream.writeln()
stream.tagContents("expected", "%4f" % self.totalHomsExp)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.totalChisqHoms)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.chisqHomsPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('homozygotes')
stream.writeln()
if self.flagHets == 1:
stream.opentag('heterozygotes')
stream.writeln()
stream.tagContents("observed", "%d" % self.totalHetsObs)
stream.writeln()
stream.tagContents("expected", "%4f" % self.totalHetsExp)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.totalChisqHets)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.chisqHetsPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('heterozygotes')
stream.writeln()
# loop for heterozygotes by allele
stream.opentag('heterozygotesByAllele')
stream.writeln()
for allele in self.hetsChisqByAllele.keys():
stream.opentag('allele', name=allele)
stream.writeln()
stream.tagContents("observed", "%d" % self.hetsObservedByAllele[allele])
stream.writeln()
stream.tagContents("expected", "%4f" % self.hetsExpectedByAllele[allele])
stream.writeln()
stream.tagContents("chisq", "%4f" % self.hetsChisqByAllele[allele])
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.hetsPvalByAllele[allele])
stream.writeln()
stream.closetag('allele')
stream.writeln()
stream.closetag('heterozygotesByAllele')
stream.writeln()
if self.flagLumps == 1:
stream.opentag('lumped')
stream.writeln()
stream.tagContents("observed", "%d" % self.lumpedObservedGenotypes)
stream.writeln()
stream.tagContents("expected", "%4f" % self.lumpedExpectedGenotypes)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.lumpedChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.lumpedChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "1")
stream.writeln()
stream.closetag('lumped')
stream.writeln()
else:
if self.flagNoRareGenotypes == 1:
stream.emptytag('lumped', role='no-rare-genotypes')
elif self.flagTooFewExpected == 1:
stream.emptytag('lumped', role='too-few-expected')
else:
stream.emptytag('lumped', role='not-calculated')
if self.flagCommons == 1:
stream.opentag('common')
stream.writeln()
stream.tagContents("observed", "%d" % self.commonObservedAccumulator)
stream.writeln()
stream.tagContents("expected", "%4f" % self.commonExpectedAccumulator)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.HWChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.HWChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "%d" % int(self.HWChisqDf))
stream.writeln()
stream.closetag('common')
stream.writeln()
else:
if self.flagNoCommonGenotypes == 1:
stream.emptytag('common', role='no-common-genotypes')
elif self.flagTooManyParameters == 1:
stream.emptytag('common', role='too-many-parameters')
else:
stream.emptytag('common', role='not-calculated')
stream.writeln()
if self.flagCommonPlusLumped == 1:
stream.opentag('commonpluslumped')
stream.writeln()
stream.tagContents("observed", "%d" % self.commonPlusLumpedObserved)
stream.writeln()
stream.tagContents("expected", "%4f" % self.commonPlusLumpedExpected)
stream.writeln()
stream.tagContents("chisq", "%4f" % self.commonPlusLumpedChisq)
stream.writeln()
stream.tagContents("pvalue", "%4f" % self.commonPlusLumpedChisqPval)
stream.writeln()
stream.tagContents("chisqdf", "%d" % int(self.commonPlusLumpedChisqDf))
stream.writeln()
stream.closetag('commonpluslumped')
stream.writeln()
else:
stream.emptytag('commonpluslumped', role='not-calculated')
stream.writeln()
stream.closetag('hardyweinberg')
# extra spacer line
stream.writeln()