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Bug fixes for mixed none/valued attributes. also now assigns fake float values for display, if requested, for covariates using the -plottable flag 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2253 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-12-03 23:52:35 +00:00
parent 3eea1ece7a
commit 2c7cb912f0
1 changed files with 32 additions and 10 deletions
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42
python/snpSelector.py
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@ -187,6 +187,7 @@ def calculateBins(variants, field, minValue, maxValue, partitions):
def calculateBinsForValues(values, field, minValue, maxValue, partitions):
sortedValues = sorted(values)
captureFieldRangeForPrinting(field, sortedValues)
targetBinSize = len(values) / (1.0*partitions)
#print sortedValues
@ -199,10 +200,11 @@ def calculateBinsForValues(values, field, minValue, maxValue, partitions):
for bin in binsAndSizes[1:]:
#print ' Breaks', bins
#print ' current bin', bin
curLeft = bins[-1][0]
curSize = bin[1]
prevSize = bins[-1][2]
#print curSize, prevSize
if curSize + prevSize > targetBinSize:
if curSize + prevSize > targetBinSize or (not isNumber(curLeft) and isNumber(bin[0])):
#print ' => appending', bin2Break(bin)
bins.append(bin2Break(bin))
else:
@ -253,18 +255,35 @@ def printFieldQual( category, field, left, right, variants, FPRate ):
novels = selectVariants(variants, VCFRecord.isNovel)
def p(stream):
if stream <> None:
print >> stream, ' %20s %20s %s %8d %8d %.2f %.2f %.2f %.2e %3d' % (category, field, binString(left, right), len(variants), len(novels), titv(variants), titv(novels), dbSNPRate(variants), FPRate, phredScale(FPRate)), more
print >> stream, ' %20s %20s %s %8d %8d %.2f %.2f %.2f %.2e %3d' % (category, field, binString(field, left, right), len(variants), len(novels), titv(variants), titv(novels), dbSNPRate(variants), FPRate, phredScale(FPRate)), more
p(sys.stdout)
p(RECAL_LOG)
def binString(left, right):
leftStr = str(left)
if type(left) == float: leftStr = "%.2f" % left
rightStr = "%5s" % str(right)
if type(right) == float: rightStr = "%.2f" % right
return '%8s %8s' % (leftStr, rightStr)
FIELD_RANGES = dict()
def captureFieldRangeForPrinting(field, sortedValues):
"""Finds the minimum float value in sortedValues for convenience printing in recal.log"""
#print sortedValues
floatValues = filter(isNumber, sortedValues)
if floatValues <> []:
FIELD_RANGES[field] = floatValues[0]
#print 'Setting field range to', field, FIELD_RANGES[field]
def isNumber(x):
return isinstance(x, (int, long, float))
def binString(field, left, right):
epsilon = 1e-2
leftStr = str(left)
rightStr = "%5s" % str(right)
if OPTIONS.plottableNones and not isNumber(left) and not isNumber(right) and field in FIELD_RANGES:
left = right = FIELD_RANGES[field] - epsilon
if OPTIONS.plottableNones and not isNumber(left) and isNumber(right):
left = right - epsilon
if isNumber(left): leftStr = "%.2f" % left
if isNumber(right): rightStr = "%.2f" % right
return '%8s %8s' % (leftStr, rightStr)
#
#
#
@ -371,7 +390,7 @@ class CallCmp:
HEADER = "TP FP FN FNRate Sensitivity PPV"
def __str__(self):
return '%6d %6d %6d %.2f %.2f %.2f' % (self.nTP, self.nFP, self.nFN, self.FNRate(), self.sensitivity(), self.PPV())
return '%6d %6d %6d %.3f %.3f %.3f' % (self.nTP, self.nFP, self.nFN, self.FNRate(), self.sensitivity(), self.PPV())
def variantInTruth(variant, truth):
if variant.getLoc() in truth:
@ -463,11 +482,14 @@ def setup():
parser.add_option("", "--unFilteredTruth", dest="unFilteredTruth",
action='store_true', default=False,
help="If provided, the unfiltered truth calls will be used in comparisons [default: %default]")
parser.add_option("", "--plottable", dest="plottableNones",
action='store_true', default=False,
help="If provided, will generate fake plottable points for annotations with None values -- doesn't effect the behavior of the system just makes it easy to plot outputs [default: %default]")
parser.add_option("-p", "--partitions", dest="partitions",
type='int', default=25,
help="Number of partitions to use for each feature. Don't use so many that the number of variants per bin is very low. [default: %default]")
parser.add_option("", "--maxRecordsForCovariates", dest="maxRecordsForCovariates",
type='int', default=200000,
type='int', default=2000000,
help="Derive covariate information from up to this many VCF records. For files with more than this number of records, the system downsamples the reads [default: %default]")
parser.add_option("-m", "--minVariantsPerBin", dest="minVariantsPerBin",
type='int', default=10,