def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
pulseFeaturesInAll_ = frozenset(PULSE_FEATURE_TAGS.keys())
for rg in rgs:
# Regarding RG ID: BLASR currently outputs a hex digest of
# 10 nibbles, instead of the 8 which would fit into a
# 32-bit word. So we truncate here for the purposes of
# cross-referencing within this API and the PacBioBamIndex
# API. We do check for a collision below.
rgID = int(rg["ID"][:8], 16)
rgName = rg["PU"]
ds = dict([pair.split("=") for pair in rg["DS"].split(";") if pair != ""])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], ds["SOFTWAREVERSION"]
rgChem = decodeTriple(*triple)
rgReadType = ds["READTYPE"]
readGroupTable_.append((rgID, rgName, rgReadType, rgChem))
pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(ds.keys())
self._readGroupTable = np.rec.fromrecords(
readGroupTable_,
dtype=[("ID" , np.uint32),
("MovieName" , "O"),
("ReadType" , "O"),
("SequencingChemistry", "O")])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = { rg.ID : rg
for rg in self._readGroupTable }
self._pulseFeaturesAvailable = pulseFeaturesInAll_
def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
# RGID -> ("abstract feature name" -> actual feature name)
self._baseFeatureNameMappings = {}
self._pulseFeatureNameMappings = {}
for rg in rgs:
rgID = rgAsInt(rg["ID"])
rgName = rg["PU"]
ds = dict([pair.split("=") for pair in rg["DS"].split(";") if pair != ""])
# spec: we only consider first two components of basecaller version
# in "chem" lookup
rgReadType = ds["READTYPE"]
rgChem = "unknown"
rgFrameRate = 0.0
if rgReadType != "TRANSCRIPT":
rgFrameRate = ds["FRAMERATEHZ"]
basecallerVersion = ".".join(ds["BASECALLERVERSION"].split(".")[0:2])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], basecallerVersion
rgChem = decodeTriple(*triple)
# Look for the features manifest entries within the DS tag,
# and build an "indirection layer", i.e. to get from
# "Ipd" to "Ipd:Frames"
# (This is a bit messy. Can we separate the manifest from
# the rest of the DS content?)
baseFeatureNameMapping = { key.split(":")[0] : key
for key in ds.keys()
if key in BASE_FEATURE_TAGS }
pulseFeatureNameMapping = { key.split(":")[0] : key
for key in ds.keys()
if key in PULSE_FEATURE_TAGS }
self._baseFeatureNameMappings[rgID] = baseFeatureNameMapping
self._pulseFeatureNameMappings[rgID] = pulseFeatureNameMapping
readGroupTable_.append((rgID, rgName, rgReadType, rgChem, rgFrameRate,
frozenset(baseFeatureNameMapping.iterkeys())))
self._readGroupTable = np.rec.fromrecords(
readGroupTable_,
dtype=[("ID" , np.int32),
("MovieName" , "O"),
("ReadType" , "O"),
("SequencingChemistry", "O"),
("FrameRate", float),
("BaseFeatures", "O")])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = { rg.ID : rg
for rg in self._readGroupTable }
# The base/pulse features "available" to clients of this file are the intersection
# of features available from each read group.
self._baseFeaturesAvailable = set.intersection(
*[set(mapping.keys()) for mapping in self._baseFeatureNameMappings.values()])
self._pulseFeaturesAvailable = set.intersection(
*[set(mapping.keys()) for mapping in self._pulseFeatureNameMappings.values()])
def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
pulseFeaturesInAll_ = frozenset(PULSE_FEATURE_TAGS.keys())
for rg in rgs:
rgID = rgAsInt(rg["ID"])
rgName = rg["PU"]
ds = dict([pair.split("=") for pair in rg["DS"].split(";") if pair != ""])
# spec: we only consider first two components of basecaller version
# in "chem" lookup
basecallerVersion = ".".join(ds["BASECALLERVERSION"].split(".")[0:2])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], basecallerVersion
rgChem = decodeTriple(*triple)
rgReadType = ds["READTYPE"]
# TODO(dalexander): need FRAMERATEHZ in RG::DS!
#rgFrameRate = ds["FRAMERATEHZ"]
rgFrameRate = 75.0
readGroupTable_.append((rgID, rgName, rgReadType, rgChem, rgFrameRate))
pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(ds.keys())
self._readGroupTable = np.rec.fromrecords(
readGroupTable_,
dtype=[("ID" , np.int32),
("MovieName" , "O"),
("ReadType" , "O"),
("SequencingChemistry", "O"),
("FrameRate", float)])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = { rg.ID : rg
for rg in self._readGroupTable }
self._pulseFeaturesAvailable = pulseFeaturesInAll_
def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
# RGID -> ("abstract feature name" -> actual feature name)
self._baseFeatureNameMappings = {}
self._pulseFeatureNameMappings = {}
for rg in rgs:
rgID = rgAsInt(rg["ID"])
rgName = rg["PU"]
ds = dict([pair.split("=") for pair in rg["DS"].split(";") if pair != ""])
# spec: we only consider first two components of basecaller version
# in "chem" lookup
basecallerVersion = ".".join(ds["BASECALLERVERSION"].split(".")[0:2])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], basecallerVersion
rgChem = decodeTriple(*triple)
rgReadType = ds["READTYPE"]
rgFrameRate = ds["FRAMERATEHZ"]
# Look for the features manifest entries within the DS tag,
# and build an "indirection layer", i.e. to get from
# "Ipd" to "Ipd:Frames"
# (This is a bit messy. Can we separate the manifest from
# the rest of the DS content?)
baseFeatureNameMapping = { key.split(":")[0] : key
for key in ds.keys()
if key in BASE_FEATURE_TAGS }
pulseFeatureNameMapping = { key.split(":")[0] : key
for key in ds.keys()
if key in PULSE_FEATURE_TAGS }
self._baseFeatureNameMappings[rgID] = baseFeatureNameMapping
self._pulseFeatureNameMappings[rgID] = pulseFeatureNameMapping
readGroupTable_.append((rgID, rgName, rgReadType, rgChem, rgFrameRate,
frozenset(baseFeatureNameMapping.iterkeys())))
self._readGroupTable = np.rec.fromrecords(
readGroupTable_,
dtype=[("ID" , np.int32),
("MovieName" , "O"),
("ReadType" , "O"),
("SequencingChemistry", "O"),
("FrameRate", float),
("BaseFeatures", "O")])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = { rg.ID : rg
for rg in self._readGroupTable }
# The base/pulse features "available" to clients of this file are the intersection
# of features available from each read group.
self._baseFeaturesAvailable = set.intersection(
*[set(mapping.keys()) for mapping in self._baseFeatureNameMappings.values()])
self._pulseFeaturesAvailable = set.intersection(
*[set(mapping.keys()) for mapping in self._pulseFeatureNameMappings.values()])
def sequencingChemistry(self):
"""
Find the name of the chemistry by consulting, in order of preference:
1) Barcode triple in file
2) "SequencingChemistry" attr in file (chemistry override)
3) metadata.xml companion file
"""
if self._sequencingChemistry is None:
triple = self._chemistryBarcodeTripleInFile
if triple is not None:
self._sequencingChemistry = decodeTriple(*triple)
elif "SequencingChemistry" in self.file["/ScanData/RunInfo"].attrs:
self._sequencingChemistry = self.file["/ScanData/RunInfo"].attrs["SequencingChemistry"]
else:
tripleFromXML = self._chemistryBarcodeTripleFromMetadataXML
if tripleFromXML is not None:
self._sequencingChemistry = decodeTriple(*tripleFromXML)
else:
raise ChemistryLookupError("Chemistry information could not be found for this file")
return self._sequencingChemistry
def sequencingChemistry(self):
"""
Find the name of the chemistry by consulting, in order of preference:
1) Barcode triple in file
2) "SequencingChemistry" attr in file (chemistry override)
3) metadata.xml companion file
"""
if self._sequencingChemistry is None:
triple = self._chemistryBarcodeTripleInFile
if triple is not None:
self._sequencingChemistry = decodeTriple(*triple)
elif "SequencingChemistry" in self.file["/ScanData/RunInfo"].attrs:
self._sequencingChemistry = self.file["/ScanData/RunInfo"].attrs["SequencingChemistry"]
else:
tripleFromXML = self._chemistryBarcodeTripleFromMetadataXML
if tripleFromXML is not None:
self._sequencingChemistry = decodeTriple(*tripleFromXML)
else:
raise ChemistryLookupError, "Chemistry information could not be found for this file"
return self._sequencingChemistry
def sequencingChemistry(self):
if self._sequencingChemistry is None:
mi = self.file["/MovieInfo"]
if (("BindingKit" in mi) and ("SequencingKit" in mi)
and ("SoftwareVersion" in mi)):
# New way
self._sequencingChemistry = \
[ decodeTriple(bk, sk, sv)
for (bk, sk, sv) in zip(
mi["BindingKit"],
mi["SequencingKit"],
mi["SoftwareVersion"]) ]
elif "SequencingChemistry" in mi:
# Old way
self._sequencingChemistry = mi["SequencingChemistry"].value
else:
raise ChemistryLookupError, "Chemistry information could not be found in cmp.h5!"
return self._sequencingChemistry
def sequencingChemistry(self):
if self._sequencingChemistry is None:
mi = dict(self.file["/MovieInfo"])
if (("BindingKit" in mi) and
("SequencingKit" in mi) and
("SoftwareVersion" in mi)):
# New way
self._sequencingChemistry = \
[ decodeTriple(bk, sk, sv)
for (bk, sk, sv) in zip(
mi["BindingKit"],
mi["SequencingKit"],
mi["SoftwareVersion"]) ]
elif "SequencingChemistry" in mi:
# Old way
self._sequencingChemistry = mi["SequencingChemistry"].value
else:
raise ChemistryLookupError, "Chemistry information could not be found in cmp.h5!"
return self._sequencingChemistry
def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
pulseFeaturesInAll_ = frozenset(PULSE_FEATURE_TAGS.keys())
for rg in rgs:
rgID = rgAsInt(rg["ID"])
rgName = rg["PU"]
ds = dict([
pair.split("=") for pair in rg["DS"].split(";") if pair != ""
])
# spec: we only consider first two components of basecaller version
# in "chem" lookup
basecallerVersion = ".".join(
ds["BASECALLERVERSION"].split(".")[0:2])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], basecallerVersion
rgChem = decodeTriple(*triple)
rgReadType = ds["READTYPE"]
# TODO(dalexander): need FRAMERATEHZ in RG::DS!
#rgFrameRate = ds["FRAMERATEHZ"]
rgFrameRate = 75.0
readGroupTable_.append(
(rgID, rgName, rgReadType, rgChem, rgFrameRate))
pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(ds.keys())
self._readGroupTable = np.rec.fromrecords(readGroupTable_,
dtype=[
("ID", np.int32),
("MovieName", "O"),
("ReadType", "O"),
("SequencingChemistry",
"O"),
("FrameRate", float)
])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = {rg.ID: rg for rg in self._readGroupTable}
self._pulseFeaturesAvailable = pulseFeaturesInAll_
def _loadReadGroupInfo(self):
rgs = self.peer.header["RG"]
readGroupTable_ = []
pulseFeaturesInAll_ = frozenset(PULSE_FEATURE_TAGS.keys())
for rg in rgs:
# Regarding RG ID: BLASR currently outputs a hex digest of
# 10 nibbles, instead of the 8 which would fit into a
# 32-bit word. So we truncate here for the purposes of
# cross-referencing within this API and the PacBioBamIndex
# API. We do check for a collision below.
rgID = int(rg["ID"][:8], 16)
rgName = rg["PU"]
ds = dict([
pair.split("=") for pair in rg["DS"].split(";") if pair != ""
])
triple = ds["BINDINGKIT"], ds["SEQUENCINGKIT"], ds[
"SOFTWAREVERSION"]
rgChem = decodeTriple(*triple)
rgReadType = ds["READTYPE"]
readGroupTable_.append((rgID, rgName, rgReadType, rgChem))
pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(ds.keys())
self._readGroupTable = np.rec.fromrecords(readGroupTable_,
dtype=[
("ID", np.uint32),
("MovieName", "O"),
("ReadType", "O"),
("SequencingChemistry",
"O")
])
assert len(set(self._readGroupTable.ID)) == len(self._readGroupTable), \
"First 8 chars of read group IDs must be unique!"
self._readGroupDict = {rg.ID: rg for rg in self._readGroupTable}
self._pulseFeaturesAvailable = pulseFeaturesInAll_
def sequencingChemistry(self):
return decodeTriple(*self.chemistryBarcodeTriple)
def sequencingChemistry(self):
return decodeTriple(*self.chemistryBarcodeTriple)
