def __init__(self, file, revcomp=False, name="", gap=None, lookahead=None, contig=None):
SeqFile.__init__(self,file,revcomp,name,gap)
self.lookahead = lookahead
if (contig == None): contig = 1
assert (contig >= 1), "contig %d is not legal" % contig
# nota bene: certainly not the most efficient or elegant implementation
currContig = 1
while (True):
if (self.lookahead != None):
(line,self.lookahead) = (self.lookahead,None)
else:
line = self.file.readline()
if (line == ""): break
if not line:
break
if (line.startswith(">")):
if (self.text != None):
if (currContig == contig):
self.lookahead = line # (next sequence header)
break
currContig += 1
self.name = self.extract_name(line[1:])
self.text = []
continue
line = line.split() # (remove whitespace)
if (self.text == None): self.text = line # (allows headerless fasta)
else: self.text.extend(line)
assert (currContig == contig), \
"contig %d is not legal (file contains only %d)" % (contig,currContig)
if (self.text != None):
self.text = "".join(self.text)
self.length = len(self.text)
def __init__(self, file, revcomp=False, name="", gap=None, codebook=None):
SeqFile.__init__(self, file, revcomp, name, gap)
if (gap == None): self.gap = chr(0)
assert (revcomp == False
), "reverse complement is not supported for qdna files"
self.codebook = codebook
self.byte_order = ">"
magic = struct.unpack(">L", file.read(4))[0]
if (magic != qdnaMagic):
if (magic == qdnaMagicSwap):
self.byte_order = "<"
else:
raise ValueError("not a quantum-dna file (magic=%08X)" % magic)
self.magic = magic
# process header
self.version = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
if (self.version not in [0x100, 0x200]):
raise ValueError("unsupported quantum-dna (version=%08X)" %
self.version)
self.headerLength = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
if (self.headerLength < 0x10):
raise ValueError("unsupported quantum-dna (header len=%08X)" %
self.headerLength)
if (self.version == 0x100) and (self.headerLength != 0x10):
raise ValueError(
"unsupported quantum-dna (version 1.0 header len=%08X)" %
self.headerLength)
self.seqOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.nameOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.length = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.propOffset = 0
if (self.headerLength >= 0x14):
self.propOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.name = ""
if (self.nameOffset != 0):
self.file.seek(self.nameOffset)
self.name = self.read_string()
if (self.propOffset != 0):
self.file.seek(self.propOffset)
while (True):
name = self.read_string()
if (len(name) == 0): break
value = self.read_string()
self.set_property(name, value)
def __init__(self, file, revcomp=False, name="", gap=None):
SeqFile.__init__(self,file,revcomp,name,gap)
self.byte_order = ">"
magic = struct.unpack(">L", file.read(NIB_MAGIC_SIZE))[0]
if (magic != NIB_MAGIC_NUMBER):
if magic == NIB_MAGIC_NUMBER_SWAP: self.byte_order = "<"
else: raise "Not a NIB file"
self.magic = magic
self.length = struct.unpack("%sL" % self.byte_order, file.read(NIB_LENGTH_SIZE))[0]
def __init__(self, file, revcomp=False, name="", gap=None, codebook=None):
SeqFile.__init__(self,file,revcomp,name,gap)
if (gap == None): self.gap = chr(0)
assert (revcomp == False), "reverse complement is not supported for qdna files"
self.codebook = codebook
self.byte_order = ">"
magic = struct.unpack(">L", file.read(4))[0]
if (magic != qdnaMagic):
if (magic == qdnaMagicSwap):
self.byte_order = "<"
else:
raise ValueError("not a quantum-dna file (magic=%08X)" % magic)
self.magic = magic
# process header
self.version = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
if (self.version not in [0x100,0x200]):
raise ValueError("unsupported quantum-dna (version=%08X)" % self.version)
self.headerLength = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
if (self.headerLength < 0x10):
raise ValueError("unsupported quantum-dna (header len=%08X)" % self.headerLength)
if (self.version == 0x100) and (self.headerLength != 0x10):
raise ValueError("unsupported quantum-dna (version 1.0 header len=%08X)" % self.headerLength)
self.seqOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.nameOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.length = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.propOffset = 0
if (self.headerLength >= 0x14):
self.propOffset = struct.unpack("%sL" % self.byte_order,
self.file.read(4))[0]
self.name = ""
if (self.nameOffset != 0):
self.file.seek(self.nameOffset)
self.name = self.read_string()
if (self.propOffset != 0):
self.file.seek(self.propOffset)
while (True):
name = self.read_string()
if (len(name) == 0): break
value = self.read_string()
self.set_property(name,value)
def __init__(self,
file,
revcomp=False,
name="",
gap=None,
lookahead=None,
contig=None):
SeqFile.__init__(self, file, revcomp, name, gap)
self.lookahead = lookahead
if (contig is None):
contig = 1
assert (contig >= 1), "contig %d is not legal" % contig
# nota bene: certainly not the most efficient or elegant implementation
currContig = 1
while (True):
if (self.lookahead is not None):
(line, self.lookahead) = (self.lookahead, None)
else:
line = self.file.readline()
if not isinstance(line, str):
line = line.decode()
if (line == ""):
break
if not line:
break
if (line.startswith(">")):
if (self.text is not None):
if (currContig == contig):
self.lookahead = line # (next sequence header)
break
currContig += 1
self.name = self.extract_name(line[1:])
self.text = []
continue
line = line.split() # (remove whitespace)
if (self.text is None):
self.text = line # (allows headerless fasta)
else:
self.text.extend(line)
assert (currContig == contig), \
"contig %d is not legal (file contains only %d)" % (contig, currContig)
if (self.text is not None):
self.text = "".join(self.text)
self.length = len(self.text)
