def _getUrl(self, exp, norm):
if not exp:
return None, None, None
assay = "DNase"
if exp.isH3K27ac():
assay = "H3K27ac"
elif exp.isH3K4me3():
assay = " H3K4me3"
bigWigs = bigWigFilters(self.assembly, exp.files)
if not bigWigs:
if "mm10" == self.assembly:
bigWigs = bigWigFilters("mm10-minimal", exp.files)
if not bigWigs:
raise Exception("missing bigWigs for " + exp.encodeID +
" assembly " + self.assembly)
bigWig = bigWigs[0]
url = bigWig.url
if "encodeproject" in url:
if not url.endswith("?proxy=true"):
url += "?proxy=true"
if self.urlStatus.find(url) and not self.urlStatus.get(url):
url = os.path.join(BIB5, "data", bigWig.expID,
bigWig.fileID + ".bigWig")
if 0 and norm:
if "mm10" == self.assembly:
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
if bigWig.expID.startswith("EN"):
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
url = os.path.join(
BIB5, "roadmap_norm/consolidated/", bigWig.expID,
bigWig.fileID + '-' + assay + ".fc.signal.norm.bigWig")
if exp.isH3K27ac():
name = "H3K27ac Signal"
color = EncodeTrackhubColors.H3K27ac_Signal.rgb
elif exp.isH3K4me3():
name = "H3K4me3 Signal"
color = EncodeTrackhubColors.H3K4me3_Signal.rgb
elif exp.isDNaseSeq():
name = "DNase Signal"
color = EncodeTrackhubColors.DNase_Signal.rgb
else:
raise Exception("unexpected exp")
return url, name, color
def process(args, expID):
exp = MetadataWS.exp(expID)
try:
bigWigs = bigWigFilters(args.assembly, exp.files)
if not bigWigs:
return
bigWig = bigWigs[0]
bigWigFnp = bigWig.fnp()
if os.path.exists(bigWig.normFnp()):
print "skipping", exp
return 0
else:
print "missing", bigWig.normFnp()
bwAssembly = bigWig.assembly
if not bigWigFnp:
print exp.getSingleBigWigSingleFnp(args)
print "missing", exp
else:
cmds = [normBin,
"--assembly=" + bwAssembly,
"--bwFnp=" + bigWig.normFnp(),
bigWigFnp]
print " ".join(cmds)
print Utils.runCmds(cmds)
return 0
except Exception, e:
print "bad " + str(e)
def process(args, expID):
exp = MetadataWS.exp(expID)
try:
bigWigs = bigWigFilters(args.assembly, exp.files)
if not bigWigs:
return
bigWig = bigWigs[0]
bigWigFnp = bigWig.fnp()
if os.path.exists(bigWig.normFnp()):
print "skipping", exp
return 0
else:
print "missing", bigWig.normFnp()
bwAssembly = bigWig.assembly
if not bigWigFnp:
print exp.getSingleBigWigSingleFnp(args)
print "missing", exp
else:
cmds = [
normBin, "--assembly=" + bwAssembly,
"--bwFnp=" + bigWig.normFnp(), bigWigFnp
]
print " ".join(cmds)
print Utils.runCmds(cmds)
return 0
except Exception, e:
print "bad " + str(e)
def _getUrl(self, exp, norm):
if not exp:
return None, None, None
assay = "DNase"
if exp.isH3K27ac():
assay = "H3K27ac"
elif exp.isH3K4me3():
assay = "H3K4me3"
bigWigs = bigWigFilters(self.assembly, exp.files)
if not bigWigs:
raise Exception("missing bigWigs for " + exp.encodeID)
bigWig = bigWigs[0]
url = bigWig.url
if 1: # self.urlStatus.find(url) and not self.urlStatus.get(url):
url = os.path.join(BIB5, "data", bigWig.expID,
bigWig.fileID + ".bigWig")
if not bigWig.expID.startswith("EN"):
url = os.path.join(
"http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/",
bigWig.fileID + '-' + assay + ".fc.signal.bigwig")
if norm:
if "mm10" == self.assembly:
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
if bigWig.expID.startswith("EN"):
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
url = os.path.join(
BIB5, "roadmap_norm/consolidated/", bigWig.expID,
bigWig.fileID + '-' + assay + ".fc.signal.norm.bigWig")
if exp.isH3K27ac():
name = "H3K27ac Signal"
color = EncodeTrackhubColors.H3K27ac_Signal.rgb
elif exp.isH3K4me3():
name = "H3K4me3 Signal"
color = EncodeTrackhubColors.H3K4me3_Signal.rgb
elif exp.isDNaseSeq():
name = "DNase Signal"
color = EncodeTrackhubColors.DNase_Signal.rgb
else:
raise Exception("unexpected exp")
return url, name, color
def _getUrl(self, exp, norm):
if not exp:
return None, None, None
assay = "DNase"
if exp.isH3K27ac():
assay = "H3K27ac"
elif exp.isH3K4me3():
assay = "H3K4me3"
bigWigs = bigWigFilters(self.assembly, exp.files)
if not bigWigs:
raise Exception("missing bigWigs for " + exp.encodeID)
bigWig = bigWigs[0]
url = bigWig.url
if 1: # self.urlStatus.find(url) and not self.urlStatus.get(url):
url = os.path.join(BIB5, "data", bigWig.expID,
bigWig.fileID + ".bigWig")
if not bigWig.expID.startswith("EN"):
url = os.path.join("http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/",
bigWig.fileID + '-' + assay + ".fc.signal.bigwig")
if norm:
if "mm10" == self.assembly:
url = os.path.join(BIB5, "encode_norm", bigWig.expID, bigWig.fileID + ".norm.bigWig")
else:
if bigWig.expID.startswith("EN"):
url = os.path.join(BIB5, "encode_norm", bigWig.expID, bigWig.fileID + ".norm.bigWig")
else:
url = os.path.join(BIB5, "roadmap_norm/consolidated/",
bigWig.expID,
bigWig.fileID + '-' + assay + ".fc.signal.norm.bigWig")
if exp.isH3K27ac():
name = "H3K27ac Signal"
color = EncodeTrackhubColors.H3K27ac_Signal.rgb
elif exp.isH3K4me3():
name = "H3K4me3 Signal"
color = EncodeTrackhubColors.H3K4me3_Signal.rgb
elif exp.isDNaseSeq():
name = "DNase Signal"
color = EncodeTrackhubColors.DNase_Signal.rgb
else:
raise Exception("unexpected exp")
return url, name, color
def process(assembly, exp):
bigWigs = bigWigFilters(assembly, exp.files)
if not bigWigs:
if "mm10" == assembly:
bigWigs = [TempWrap(exp.encodeID, eidToBigWigFileID[exp.encodeID])]
if not bigWigs:
print "missing bigWigs for " + exp.encodeID
return
if 0 and len(bigWigs) > 1:
print "weird", bigWigs
sys.exit(1)
bigWig = bigWigs[0]
if "eid" in bigWig.fnp():
return # ignore Roadmap for now
print bigWig.fnp()
def process(assembly, exp):
bigWigs = bigWigFilters(assembly, exp.files)
if not bigWigs:
if "mm10" == assembly:
bigWigs = [TempWrap(exp.encodeID,
eidToBigWigFileID[exp.encodeID])]
if not bigWigs:
print "missing bigWigs for " + exp.encodeID
return
if 0 and len(bigWigs) > 1:
print "weird", bigWigs
sys.exit(1)
bigWig = bigWigs[0]
if "eid" in bigWig.fnp():
return # ignore Roadmap for now
print bigWig.fnp()
def _getUrl(self, exp, norm):
if not exp:
return None, None, None
assay = "DNase"
if exp.isH3K4me3():
assay = "H3K4me3"
bigWigs = bigWigFilters(self.assembly, exp.files)
if not bigWigs:
raise Exception("missing bigWigs for " + exp.encodeID)
bigWig = bigWigs[0]
url = bigWig.url
if self.urlStatus.find(url) and not self.urlStatus.get(url):
url = os.path.join(BIB5, "data", bigWig.expID,
bigWig.fileID + ".bigWig")
if norm:
if "mm10" == self.assembly:
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
if bigWig.expID.startswith("EN"):
url = os.path.join(BIB5, "encode_norm", bigWig.expID,
bigWig.fileID + ".norm.bigWig")
else:
url = os.path.join(
BIB5, "roadmap_norm/consolidated/", bigWig.expID,
bigWig.fileID + '-' + assay + ".fc.signal.norm.bigWig")
if exp.isH3K4me3():
name = "H3K4me3 Signal"
color = "18,98,235"
elif exp.isDNaseSeq():
name = "DNase Signal"
color = "255,121,3"
else:
raise Exception("unexpected exp")
return url, name, color
def _getUrl(self, exp, norm):
if not exp:
return None, None, None
assay = "DNase"
if exp.isH3K4me3():
assay = "H3K4me3"
bigWigs = bigWigFilters(self.assembly, exp.files)
if not bigWigs:
raise Exception("missing bigWigs for " + exp.encodeID)
bigWig = bigWigs[0]
url = bigWig.url
if 1: # self.urlStatus.find(url) and not self.urlStatus.get(url):
url = os.path.join(BIB5, "data", bigWig.expID,
bigWig.fileID + ".bigWig")
if norm:
if "mm10" == self.assembly:
url = os.path.join(BIB5, "encode_norm", bigWig.expID, bigWig.fileID + ".norm.bigWig")
else:
if bigWig.expID.startswith("EN"):
url = os.path.join(BIB5, "encode_norm", bigWig.expID, bigWig.fileID + ".norm.bigWig")
else:
url = os.path.join(BIB5, "roadmap_norm/consolidated/",
bigWig.expID,
bigWig.fileID + '-' + assay + ".fc.signal.norm.bigWig")
if exp.isH3K4me3():
name = "H3K4me3 Signal"
color = "18,98,235"
elif exp.isDNaseSeq():
name = "DNase Signal"
color = "255,121,3"
else:
raise Exception("unexpected exp")
return url, name, color