class GenomePartition(object):
"object to store info about genome and partition it into windows"
def __init__(self, db, genomeFileSpec, winSize, overlap, maxGap,
minUnplacedSize=0, liftFile=None, unplacedChroms=None):
self.db = db
self.seqs = GenomeSeqs(db, genomeFileSpec)
# flag unplaced chroms before loading lift, as it changes
# partitioning
if unplacedChroms != None:
unplacedChroms.flagSeqs(self.seqs)
if liftFile != None:
self.seqs.defineSeqRegionsFromLifts(liftFile)
self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap,
minUnplacedSize)
def dump(self, fh):
"print info about object"
fh.write("=========== GENOME REGIONS ===========\n")
self.seqs.dump(fh)
fh.write("=========== WINDOWS ===========\n")
self.windows.dump(fh)
fh.flush()
class GenomePartition(object):
"object to store info about genome and partition it into windows"
def __init__(self,
db,
genomeFileSpec,
winSize,
overlap,
maxGap,
minUnplacedSize=0,
liftFile=None,
unplacedChroms=None):
self.db = db
self.seqs = GenomeSeqs(db, genomeFileSpec)
# flag unplaced chroms before loading lift, as it changes
# partitioning
if unplacedChroms != None:
unplacedChroms.flagSeqs(self.seqs)
if liftFile != None:
self.seqs.defineSeqRegionsFromLifts(liftFile)
self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap,
minUnplacedSize)
def dump(self, fh):
"print info about object"
fh.write("=========== GENOME REGIONS ===========\n")
self.seqs.dump(fh)
fh.write("=========== WINDOWS ===========\n")
self.windows.dump(fh)
fh.flush()
def __init__(self,
db,
genomeFileSpec,
winSize,
overlap,
maxGap,
minUnplacedSize=0,
liftFile=None,
unplacedChroms=None):
self.db = db
self.seqs = GenomeSeqs(db, genomeFileSpec)
# flag unplaced chroms before loading lift, as it changes
# partitioning
if unplacedChroms != None:
unplacedChroms.flagSeqs(self.seqs)
if liftFile != None:
self.seqs.defineSeqRegionsFromLifts(liftFile)
self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap,
minUnplacedSize)
def __init__(self, db, genomeFileSpec, winSize, overlap, maxGap,
minUnplacedSize=0, liftFile=None, unplacedChroms=None):
self.db = db
self.seqs = GenomeSeqs(db, genomeFileSpec)
# flag unplaced chroms before loading lift, as it changes
# partitioning
if unplacedChroms != None:
unplacedChroms.flagSeqs(self.seqs)
if liftFile != None:
self.seqs.defineSeqRegionsFromLifts(liftFile)
self.windows = GenomeWindows(self.seqs, winSize, overlap, maxGap,
minUnplacedSize)
