def __iter__(self):
handle = self._handle
handle.seek(0)
id = None
start_offset = handle.tell()
line = handle.readline()
if not line:
#Empty file!
return
at_char = _as_bytes("@")
plus_char = _as_bytes("+")
if line[0:1] != at_char:
raise ValueError("Problem with FASTQ @ line:\n%s" % repr(line))
while line:
#assert line[0]=="@"
#This record seems OK (so far)
id = line[1:].rstrip()
#Find the seq line(s)
seq_len = 0
length = len(line)
while line:
line = handle.readline()
length += len(line)
if line.startswith(plus_char) : break
seq_len += len(line.strip())
if not line:
raise ValueError("Premature end of file in seq section")
#assert line[0]=="+"
#Find the qual line(s)
qual_len = 0
while line:
if seq_len == qual_len:
#Should be end of record...
end_offset = handle.tell()
line = handle.readline()
if line and line[0:1] != at_char:
ValueError("Problem with line %s" % repr(line))
break
else:
line = handle.readline()
qual_len += len(line.strip())
length += len(line)
if seq_len != qual_len:
raise ValueError("Problem with quality section")
yield _bytes_to_string(id), start_offset, length
start_offset = end_offset
def get_raw(self, offset):
"""Similar to the get method, but returns the record as a raw
string."""
# TODO - Refactor this and the __init__ method to reduce code
# duplication?
handle = self._handle
handle.seek(offset)
line = handle.readline()
data = line
at_char = _as_bytes("@")
plus_char = _as_bytes("+")
if line[0:1] != at_char:
raise ValueError("Problem with FASTQ @ line:\n%s" % repr(line))
# Find the seq line(s)
seq_len = 0
while line:
line = handle.readline()
data += line
if line.startswith(plus_char):
break
seq_len += len(line.strip())
if not line:
raise ValueError("Premature end of file in seq section")
assert line[0:1] == plus_char
# Find the qual line(s)
qual_len = 0
while line:
if seq_len == qual_len:
# Should be end of record...
pos = handle.tell()
line = handle.readline()
if line and line[0:1] != at_char:
ValueError("Problem with line %s" % repr(line))
break
else:
line = handle.readline()
data += line
qual_len += len(line.strip())
if seq_len != qual_len:
raise ValueError("Problem with quality section")
return data
def get_raw(self, offset):
"""Similar to the get method, but returns the record as a raw
string."""
# TODO - Refactor this and the __init__ method to reduce code
# duplication?
handle = self._handle
handle.seek(offset)
line = handle.readline()
data = line
at_char = _as_bytes("@")
plus_char = _as_bytes("+")
if line[0:1] != at_char:
raise ValueError("Problem with FASTQ @ line:\n%s" % repr(line))
# Find the seq line(s)
seq_len = 0
while line:
line = handle.readline()
data += line
if line.startswith(plus_char):
break
seq_len += len(line.strip())
if not line:
raise ValueError("Premature end of file in seq section")
assert line[0:1] == plus_char
# Find the qual line(s)
qual_len = 0
while line:
if seq_len == qual_len:
# Should be end of record...
pos = handle.tell()
line = handle.readline()
if line and line[0:1] != at_char:
ValueError("Problem with line %s" % repr(line))
break
else:
line = handle.readline()
data += line
qual_len += len(line.strip())
if seq_len != qual_len:
raise ValueError("Problem with quality section")
return data
