def _makeMainTrackDb(self):
mainTrackDb = []
for atn, labelNAndInfo in self.byAssayBiosampleType.iteritems():
pri = self.priority.increment(1)
totalExperiments = sum(
[len(info["exps"]) for info in labelNAndInfo.values()])
shortLabel = self.labelNToNormal[atn]
longLabel = self.labelNToNormal[
atn] + " (%s experiments)" % totalExperiments
mainTrackDb.append("""
track super_{atn}
superTrack on
priority {priority}
shortLabel {shortL}
longLabel {longL}
description {longL}
""".format(atn=atn,
priority=pri,
shortL=shortLabel,
longL=Helpers.makeLongLabel(longLabel)))
outF = StringIO.StringIO()
outF.write('\n'.join(mainTrackDb))
for atn, labelNAndInfo in self.byAssayBiosampleType.iteritems():
for labelN, info in labelNAndInfo.iteritems():
with open(info["fnp"]) as f:
outF.write(f.read())
outF.write('\n')
return outF.getvalue()
def _makeMainTrackDb(self):
mainTrackDb = []
for atn, btAndInfo in self.byAssayBiosampleType.iteritems():
pri = self.priority.increment(1)
totalExperiments = 0
for bt, info in btAndInfo.iteritems():
if "0_all" != bt:
totalExperiments += len(info["exps"])
shortLabel = self.btToNormal[atn]
longLabel = info["longLabelBase"] + " (%s experiments)" % totalExperiments
mainTrackDb.append("""
track super_{atn}
superTrack on
priority {priority}
shortLabel {shortL}
longLabel {longL}
""".format(atn = atn,
priority = pri,
shortL=shortLabel,
longL=Helpers.makeLongLabel(longLabel)))
outF = StringIO.StringIO()
outF.write('\n'.join(mainTrackDb))
for atn, btAndInfo in self.byAssayBiosampleType.iteritems():
for bt, info in btAndInfo.iteritems():
with open(info["fnp"]) as f:
outF.write(f.read())
outF.write('\n')
return outF.getvalue()
def _makeMainTrackDb(self):
mainTrackDb = []
for bt, btnFnps in self.byBiosampleTypeBiosample.iteritems():
pri = self.priority.increment(1)
totalExperiments = sum(
[len(info["expIDs"]) for info in btnFnps.values()])
shortLabel = self.btToNormal[bt]
longLabel = self.btToNormal[
bt] + " (%s experiments)" % totalExperiments
if shortLabel == "induced pluripotent stem cell line":
shortLabel = "IPSC"
shortLabel = titlecase(shortLabel)
shortLabel = shortLabel.replace('Ipsc', 'IPSC')
shortLabel = shortLabel.replace('In Vitro Differentiated Cell',
'in vitro Diff Cell')
shortLabel = shortLabel + ' Experiments'
mainTrackDb.append("""
track super_{bt}
superTrack on
priority {priority}
shortLabel {shortL}
longLabel {longL}
description {longL}
""".format(bt=bt,
priority=pri,
shortL=shortLabel,
longL=Helpers.makeLongLabel(longLabel)))
outF = StringIO.StringIO()
outF.write('\n'.join(mainTrackDb))
for bt, btnFnps in self.byBiosampleTypeBiosample.iteritems():
for btn, info in btnFnps.iteritems():
with open(info["fnp"]) as f:
outF.write(f.read())
outF.write('\n')
return outF.getvalue()
def outputCompositeTrackByBiosampleType(assembly, bt, btn, expIDs, fnp, idx,
total, subGroups, biosample_type,
biosample_term_name, lookupByExp):
if not os.path.exists(fnp):
raise Exception("missing " + fnp)
subGroupsDict = {}
for k in Helpers.SubGroupKeys:
subGroupsDict[k] = {a[0]: a[1] for a in subGroups[k]}
longLabel = biosample_term_name + " (%s experiments)" % len(expIDs)
if "cell_line" == bt:
subGroup1key = "target_label"
subGroup2key = "biosample_summary"
else:
subGroup1key = "target_label"
subGroup2key = "age_sex"
subGroup3key = "view"
subGroup1 = Helpers.unrollEquals(subGroupsDict[subGroup1key])
subGroup2 = Helpers.unrollEquals(subGroupsDict[subGroup2key])
subGroup3 = Helpers.unrollEquals(subGroupsDict[subGroup3key])
actives = []
for expID in expIDs:
if expID in lookupByExp:
actives.append(lookupByExp[expID].isActive())
isActive = any(t for t in actives)
if isActive:
print("active biosample (composite):", btn)
with open(fnp) as f:
subtracks = f.read()
with open(fnp, 'w') as f:
f.write("""
track {bt}_{btn}
parent super_{bt}
compositeTrack on
centerLabelsDense on
""".format(bt=bt, btn=btn))
if isActive:
f.write("visibility full\n")
f.write("""shortLabel {shortL}
description {longL}
longLabel {longL}
type bigWig 9 +
maxHeightPixels 64:12:8
autoScale on
subGroup1 {subGroup1key} {subGroup1key} {subGroup1}
subGroup2 {subGroup2key} {subGroup2key} {subGroup2}
subGroup3 {subGroup3key} {subGroup3key} {subGroup3}
sortOrder {subGroup1key}=+ {subGroup2key}=+ {subGroup3key}=+
dimensions dimX={subGroup2key} dimY={subGroup1key}
dragAndDrop subTracks
hoverMetadata on
darkerLabels on
""".format(shortL=Helpers.makeShortLabel(biosample_term_name),
longL=Helpers.makeLongLabel(longLabel),
subGroup1key=subGroup1key,
subGroup1=subGroup1,
subGroup2key=subGroup2key,
subGroup2=subGroup2,
subGroup3key=subGroup3key,
subGroup3=subGroup3))
f.write('\n' + subtracks)
printWroteNumLines(fnp, idx, 'of', total)
def outputCompositeTrackByBiosampleType(assembly, assay_term_name, atn, biosample_type, bt,
exps, fnp, idx, total, subGroups, lookupByExp, longLabelBase = None):
if not os.path.exists(fnp):
raise Exception("missing " + fnp)
subGroupsDict = {}
for k in Helpers.SubGroupKeys:
subGroupsDict[k] = {a[0]:a[1] for a in subGroups[k]}
longLabel = biosample_type + " (%s experiments)" % len(exps)
print(subGroupsDict["assay"])
if atn in ["dnase", "atac_seq"]:
subGroup1key = "biosample"
subGroup2key = "age"
elif "histone_modifications" == atn:
subGroup1key = "biosample"
subGroup2key = "label"
elif "transcription_factors" == atn:
subGroup1key = "biosample"
subGroup2key = "label"
elif atn in ["transcription", "rampage", "microRNAseq"]:
subGroup1key = "biosample"
subGroup2key = "assay"
else:
subGroup1key = "donor"
subGroup2key = "age"
if "0_all" == bt:
subGroup1key = "biosample"
subGroup2key = "age_sex"
subGroup3key = "view"
subGroup1 = Helpers.unrollEquals(subGroupsDict[subGroup1key])
subGroup2 = Helpers.unrollEquals(subGroupsDict[subGroup2key])
subGroup3 = Helpers.unrollEquals(subGroupsDict[subGroup3key])
with open(fnp) as f:
subtracks = f.read()
actives = []
# for expID in expIDs:
# if expID in lookupByExp:
# actives.append(lookupByExp[expID].isActive())
isActive = any(t for t in actives)
# if isActive:
# print("active biosample (composite):", btn)
with open(fnp, 'w') as f:
f.write("""
track {atn}_{bt}
parent super_{atn}
compositeTrack on
centerLabelsDense on
""".format(atn=atn,
bt=bt))
if isActive:
f.write("visibility full\n")
f.write("""shortLabel {shortL}
longLabel {longL}
type bigWig 9 +
maxHeightPixels 64:12:8
autoScale on
subGroup1 {subGroup1key} {subGroup1key} {subGroup1}
subGroup2 {subGroup2key} {subGroup2key} {subGroup2}
subGroup3 {subGroup3key} {subGroup3key} {subGroup3}
sortOrder {subGroup1key}=+ {subGroup2key}=+ {subGroup3key}=+
dimensions dimX={subGroup2key} dimY={subGroup1key}
dragAndDrop subTracks
hoverMetadata on
darkerLabels on
""".format(shortL=Helpers.makeShortLabel(biosample_type),
longL=Helpers.makeLongLabel(longLabel),
subGroup1key=subGroup1key,
subGroup1=subGroup1,
subGroup2key=subGroup2key,
subGroup2=subGroup2,
subGroup3key=subGroup3key,
subGroup3=subGroup3
))
f.write('\n' + subtracks)
printWroteNumLines(fnp, idx, 'of', total)