def _loadReferenceInfo(self):
_referenceGroupTbl = np.rec.fromrecords(
zip(self.file["/RefGroup/ID"],
self.file["/RefGroup/RefInfoID"],
[path[1:] for path in self.file["/RefGroup/Path"]]),
dtype=[("ID" , int),
("RefInfoID", int),
("Name" , object)])
_referenceInfoTbl = np.rec.fromrecords(
zip(self.file["/RefInfo/ID"],
self.file["/RefInfo/FullName"],
self.file["/RefInfo/Length"],
self.file["/RefInfo/MD5"]) ,
dtype=[("RefInfoID", int),
("FullName" , object),
("Length" , int),
("MD5" , object)])
self._referenceInfoTable = \
rec_join("RefInfoID", _referenceGroupTbl, _referenceInfoTbl, jointype="inner")
if self.isSorted:
_offsetTable = self.file["/RefGroup/OffsetTable"].value \
.view(dtype=OFFSET_TABLE_DTYPE) \
.view(np.recarray) \
.flatten()
self._referenceInfoTable = rec_join("ID",
self._referenceInfoTable,
_offsetTable,
jointype="inner")
self._referenceDict = {}
self._readLocatorByKey = {}
for record in self._referenceInfoTable:
if record.ID != -1:
assert record.ID != record.Name
shortName = splitFastaHeader(record.FullName)[0]
if (shortName in self._referenceDict or
record.ID in self._referenceDict or
record.Name in self._referenceDict or
record.FullName in self._referenceDict or
record.MD5 in self._referenceDict):
raise ValueError, "Duplicate reference contig sequence or identifier"
else:
self._referenceDict[shortName] = record
self._referenceDict[record.ID] = record
self._referenceDict[record.Name] = record
self._referenceDict[record.FullName] = record
self._referenceDict[record.MD5] = record
if self.isSorted:
readLocator = makeReadLocator(self, record.ID)
self._readLocatorByKey[record.ID] = readLocator
self._readLocatorByKey[shortName] = readLocator
def _loadReferenceInfo(self):
_referenceGroupTbl = np.rec.fromrecords(
zip(self.file["/RefGroup/ID"][:],
self.file["/RefGroup/RefInfoID"][:],
[path[1:] for path in self.file["/RefGroup/Path"]]),
dtype=[("ID" , int),
("RefInfoID", int),
("Name" , object)])
_referenceInfoTbl = np.rec.fromrecords(
zip(self.file["/RefInfo/ID"][:],
self.file["/RefInfo/FullName"][:],
self.file["/RefInfo/Length"][:],
self.file["/RefInfo/MD5"][:]) ,
dtype=[("RefInfoID", int),
("FullName" , object),
("Length" , int),
("MD5" , object)])
self._referenceInfoTable = \
rec_join("RefInfoID", _referenceGroupTbl, _referenceInfoTbl, jointype="inner")
if self.isSorted:
_offsetTable = self.file["/RefGroup/OffsetTable"].value \
.view(dtype=OFFSET_TABLE_DTYPE) \
.view(np.recarray) \
.flatten()
self._referenceInfoTable = rec_join("ID",
self._referenceInfoTable,
_offsetTable,
jointype="inner")
self._referenceDict = {}
self._readLocatorByKey = {}
# For cmp.h5 files with large numbers of references, accessing
# the recarray fields in the inner loop was terribly slow.
# This makes things faster, though the code is less
# straightforward. (One of the tradeoffs we have to make
# without a compiler to help us...)
recordID = self._referenceInfoTable.ID
recordName = self._referenceInfoTable.Name
recordFullName = self._referenceInfoTable.FullName
recordMD5 = self._referenceInfoTable.MD5
for i, record in enumerate(self._referenceInfoTable):
if recordID[i] != -1:
assert recordID[i] != record.Name
shortName = splitFastaHeader(record.FullName)[0]
if (shortName in self._referenceDict or
recordID[i] in self._referenceDict or
recordName[i] in self._referenceDict or
recordFullName[i] in self._referenceDict or
recordMD5[i] in self._referenceDict):
raise ValueError, "Duplicate reference contig sequence or identifier"
else:
self._referenceDict[shortName] = record
self._referenceDict[recordID[i]] = record
self._referenceDict[recordName[i]] = record
self._referenceDict[recordFullName[i]] = record
self._referenceDict[recordMD5[i]] = record
if self.isSorted:
readLocator = makeReadLocator(self, recordID[i])
self._readLocatorByKey[recordID[i]] = readLocator
self._readLocatorByKey[shortName] = readLocator
def _loadReferenceInfo(self):
_referenceGroupTbl = np.rec.fromrecords(zip(
self.file["/RefGroup/ID"][:], self.file["/RefGroup/RefInfoID"][:],
[path[1:] for path in self.file["/RefGroup/Path"]]),
dtype=[("ID", int),
("RefInfoID", int),
("Name", object)])
_referenceInfoTbl = np.rec.fromrecords(zip(
self.file["/RefInfo/ID"][:], self.file["/RefInfo/FullName"][:],
self.file["/RefInfo/Length"][:], self.file["/RefInfo/MD5"][:]),
dtype=[("RefInfoID", int),
("FullName", object),
("Length", int),
("MD5", object)])
self._referenceInfoTable = \
rec_join("RefInfoID", _referenceGroupTbl, _referenceInfoTbl, jointype="inner")
if self.isSorted:
_offsetTable = self.file["/RefGroup/OffsetTable"].value \
.view(dtype=OFFSET_TABLE_DTYPE) \
.view(np.recarray) \
.flatten()
self._referenceInfoTable = rec_join("ID",
self._referenceInfoTable,
_offsetTable,
jointype="inner")
self._referenceDict = {}
self._readLocatorByKey = {}
# For cmp.h5 files with large numbers of references, accessing
# the recarray fields in the inner loop was terribly slow.
# This makes things faster, though the code is less
# straightforward. (One of the tradeoffs we have to make
# without a compiler to help us...)
recordID = self._referenceInfoTable.ID
recordName = self._referenceInfoTable.Name
recordFullName = self._referenceInfoTable.FullName
recordMD5 = self._referenceInfoTable.MD5
for i, record in enumerate(self._referenceInfoTable):
if recordID[i] != -1:
assert recordID[i] != record.Name
shortName = splitFastaHeader(record.FullName)[0]
if (shortName in self._referenceDict
or recordID[i] in self._referenceDict
or recordName[i] in self._referenceDict
or recordFullName[i] in self._referenceDict
or recordMD5[i] in self._referenceDict):
raise ValueError(
"Duplicate reference contig sequence or identifier")
else:
self._referenceDict[shortName] = record
self._referenceDict[recordID[i]] = record
self._referenceDict[recordName[i]] = record
self._referenceDict[recordFullName[i]] = record
self._referenceDict[recordMD5[i]] = record
if self.isSorted:
readLocator = makeReadLocator(self, recordID[i])
self._readLocatorByKey[recordID[i]] = readLocator
self._readLocatorByKey[shortName] = readLocator
