def __init__(self, *args, **keywords):
SeqDict.__init__(self)
self.index = FastaIndex()
if len(args) > 0:
self.read(*args, **keywords)
def __init__(self, *args, ** keywords):
SeqDict.__init__(self)
self.index = FastaIndex()
if len(args) > 0:
self.read(* args, **keywords)
def __getitem__(self, key):
"""Get a sequence by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
val = self.index.get(key)
# cache value
self[key] = val
return val
else:
return val
def __getitem__(self, key):
"""Get a sequence by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
val = self.index.get(key)
# cache value
self[key] = val
return val
else:
return val
def getseq(self, key, start=1, end=None, strand=1):
"""Get a sequence (or subsequence) by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
return self.index.get(key, start, end, strand)
else:
start = util.clamp(start, 1, None)
end = util.clamp(end, 1, None)
val = val[start - 1:end]
# reverse complement if needed
if strand == -1:
val = _revcomp(val)
return val
def getseq(self, key, start=1, end=None, strand=1):
"""Get a sequence (or subsequence) by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
return self.index.get(key, start, end, strand)
else:
start = util.clamp(start, 1, None)
end = util.clamp(end, 1, None)
val = val[start-1:end]
# reverse complement if needed
if strand == -1:
val = _revcomp(val)
return val
