def __init_file_streams(self, in_arg=0, out_arg=1):
if in_arg is not None:
if len(self.args) - 1 < in_arg or self.args[in_arg] == '-':
self.infile = sys.stdin
self.from_stdin = True
else:
self.infile = self.args[in_arg]
if not os.path.isfile(self.infile):
self.error("Cannot read input file: " + self.infile)
self.infile = io.xopen(self.infile, 'r')
self.from_stdin = False
if out_arg is not None:
if len(self.args) - 1 < out_arg or self.args[out_arg] == '-':
self.outfile = sys.stdout
self.to_stdout = True
else:
self.outfile = self.args[out_arg]
if os.path.isfile(self.outfile) and not self.options.wild:
self.error("Outfile already exists, " \
"use -w/--wild to overwite")
self.outfile = io.xopen(self.outfile, 'w')
self.to_stdout = False
def __init_file_streams(self, in_arg=0, out_arg=1):
if in_arg is not None:
if len(self.args) - 1 < in_arg or self.args[in_arg] == '-':
self.infile = sys.stdin
self.from_stdin = True
else:
self.infile = self.args[in_arg]
if not os.path.isfile(self.infile):
self.error("Cannot read input file: " + self.infile)
self.infile = io.xopen(self.infile, 'r')
self.from_stdin = False
if out_arg is not None:
if len(self.args) - 1 < out_arg or self.args[out_arg] == '-':
self.outfile = sys.stdout
self.to_stdout = True
else:
self.outfile = self.args[out_arg]
if os.path.isfile(self.outfile) and not self.options.wild:
self.error("Outfile already exists, " \
"use -w/--wild to overwite")
self.outfile = io.xopen(self.outfile, 'w')
self.to_stdout = False
def parse(infile, *args, **kwargs):
if isinstance(infile, file) or isinstance(infile, GzipFile):
fh = infile
do_close = False
else:
fh = xopen(infile, 'r')
do_close = True
record = None
for idx, line in enumerate(fh):
line = line.strip()
step = idx % 4
if step == 0:
if record is not None:
yield record
record = FastqRead(id=line[1:])
if step == 1:
record.sequence = line
elif step == 2:
record.optional_id = line[1:]
else:
record.quality = line
if do_close:
fh.close()
def seek_to_start(fh, max_iter=100):
"""Moves a file handle to the first ">" in a FASTA file.
All lines that come before that are ignored.
"""
if isinstance(fh, str):
fh = xopen(fh, 'r')
fh.seek(0)
found = False
for idx,line in enumerate(fh):
if idx > max_iter:
raise Exception("Seeking passed max_iter")
line = line.strip()
if line.startswith(">"):
found = True
break
if not found:
raise Exception("Seeking past end of file")
fh.seek(0)
while idx > 0:
fh.next()
idx = idx - 1
return fh
def seek_to_start(fh, max_iter=100):
"""Moves a file handle to the first ">" in a FASTA file.
All lines that come before that are ignored.
"""
if isinstance(fh, str):
fh = xopen(fh, 'r')
fh.seek(0)
found = False
for idx, line in enumerate(fh):
if idx > max_iter:
raise Exception("Seeking passed max_iter")
line = line.strip()
if line.startswith(">"):
found = True
break
if not found:
raise Exception("Seeking past end of file")
fh.seek(0)
while idx > 0:
fh.next()
idx = idx - 1
return fh
def parse(infile, *args, **kwargs):
if isinstance(infile, file) or isinstance(infile, GzipFile):
fh = infile
do_close = False
else:
fh = xopen(infile, 'r')
do_close = True
record = None
for idx,line in enumerate(fh):
line = line.strip()
step = idx % 4
if step == 0:
if record is not None:
yield record
record = FastqRead(id=line[1:])
if step == 1:
record.sequence = line
elif step == 2:
record.optional_id = line[1:]
else:
record.quality = line
if do_close:
fh.close()
def parse(infile, *args, **kwargs):
fh = xopen(infile, 'r')
record = None
for idx,line in enumerate(fh):
yield BowtieRead.from_record(line)
fh.close()
def parse(infile, *args, **kwargs):
fh = xopen(infile, 'r')
record = None
for idx, line in enumerate(fh):
yield BowtieRead.from_record(line)
fh.close()
def parse(qseq, *args, **kwargs):
fh = xopen(qseq, 'r')
record = None
for idx,line in enumerate(fh):
yield QseqRead.from_record(line)
fh.close()
