def getScaff(self):
if self._scaffDef:
seq = zlib.decompress(self._scaffCompressed)
if self._removeNonDna:
return removeNonDna(seq)
else:
return seq
else:
return None
def getScaff(self):
if self._scaffDef:
seq = zlib.decompress(self._scaffCompressed)
if self._removeNonDna:
return removeNonDna(seq)
else:
return seq
else:
return None
def __init__(self, id, name, seq):
self.id = id
self.name = noNewLine(name)
seq = noNewLine(seq)
self.seqBp = len(removeNonDna(seq))
self._seqCompressed = zlib.compress(seq)
self._taxPathDict = None
self._placementWeight = None
self._hash = hash(seq.upper())
self._candidateTaxPathDictList = []
self._candidateTaxPathDictWeightsList = []
self._candidateTaxPathDictSourceList = [] # where does this prediction come from
self._candidateTaxPathDictTagList = []
self.scaffold = None
self._removeNonDna = False
def __init__(self, id, name, contig, scaffoldSeq):
self.id = id
self.name = name
self._taxPathDict = None
self.contigs = []
self._removeNonDna = False
if (contig != None):
self.contigs.append(contig)
if (scaffoldSeq != None):
seq = noNewLine(scaffoldSeq)
self.seqBp = len(removeNonDna(seq))
self._scaffCompressed = zlib.compress(seq)
self._hash = hash(seq.upper())
self._scaffDef = True
else:
self._scaffDef = False
self._hash = None
self.seqBp = 0
def __init__(self, id, name, contig, scaffoldSeq):
self.id = id
self.name = name
self._taxPathDict = None
self.contigs = []
self._removeNonDna = False
if (contig != None):
self.contigs.append(contig)
if (scaffoldSeq != None):
seq = noNewLine(scaffoldSeq)
self.seqBp = len(removeNonDna(seq))
self._scaffCompressed = zlib.compress(seq)
self._hash = hash(seq.upper())
self._scaffDef = True
else:
self._scaffDef = False
self._hash = None
self.seqBp = 0
def getSeq(self):
seq = zlib.decompress(self._seqCompressed)
if self._removeNonDna:
return removeNonDna(seq)
else:
return seq
def parse(self, record):
self._outFileBuffer.writeText(str('>' + str(record.id) + '\n'))
self._outFileBuffer.writeText(str(removeNonDna(str(record.seq)) + '\n'))
def parse(self, record):
self._outFileBuffer.writeText(str('>' + str(record.id) + '\n'))
self._outFileBuffer.writeText(
str(removeNonDna(str(record.seq)) + '\n'))
