def generalCREs(self, showCombo, hideAll=True):
base = os.path.join("http://bib7.umassmed.edu/~purcarom",
"encyclopedia/Version-4", "ver10", self.assembly)
if self.browser in [UCSC, ENSEMBL]:
if showCombo:
url = os.path.join(base, self.assembly + "-cREs-V10.bigBed")
t = PredictionTrack("general cREs (5 group)", self.priority,
url,
hideAll).track("general cREs (5 group)")
self.priority += 1
else:
t = ""
for assay in ["CTCF", "Enhancer", "Promoter"]:
url = os.path.join(
WWW, self.assembly + "-cRE." + assay + ".cREs.bigBed")
a = assay
if a == "Enhancer":
a = "H3K27ac"
if a == "Promoter":
a = "H3K4me3"
t += PredictionTrack(
"general cREs (9 state) " + a, self.priority, url,
hideAll).track("general cREs (9 state) " + a)
self.priority += 1
else:
url = os.path.join(base, self.assembly + "-cREs-V10.bed.gz")
t = Track("cREs", self.priority, url, type="hammock").track_washu()
self.priority += 1
return t
def trackhubExp(self, exp):
url, name, color = self._getUrl(exp, False)
desc = Track.MakeDesc(name, exp.age, exp.biosample_term_name)
track = BigWigTrack(desc, self.priority, url, color).track()
self.priority += 1
return track
def predictionTrackHub(self, wepi):
fnp = wepi.predictionFnp()
if not os.path.exists(fnp):
return None
desc = Track.MakeDesc("Promoter-like", wepi.epi.age_display,
wepi.epi.biosample_term_name)
url = os.path.join(BIB5, Dirs.promoterTracksBase,
os.path.basename(fnp))
track = PredictionTrack(desc, self.priority, url).track()
self.priority += 1
return track
def predictionTrackHub(self, wepi):
fnp = wepi.predictionFnp()
if not os.path.exists(fnp):
return None
if AssayType.Enhancer == self.assayType:
descBase = "enhancer-like"
url = os.path.join(BIB5, Dirs.enhancerTracksBase,
os.path.basename(fnp))
elif AssayType.Promoter == self.assayType:
descBase = "promoter-like"
url = os.path.join(BIB5, Dirs.promoterTracksBase,
os.path.basename(fnp))
desc = Track.MakeDesc(descBase, wepi.epi.age_display,
wepi.epi.biosample_term_name)
track = PredictionTrack(desc, self.priority, url).track(descBase)
self.priority += 1
return track