def __init__(self,refGene_fn) :
refGene_f = open(refGene_fn)
# check for header
first_line = refGene_f.next()
if not first_line.strip().startswith('#') :
refGene_f.seek(0) # first line not header, reset the file pointer
DictReader.__init__(self,refGene_f,delimiter='\t',fieldnames=RefGeneOutput.FIELD_NAMES)
def __init__(self, csvFile, csvAbleClass = CSVable, useHeader = False, encoding = None, handleComments = False, *args, **kwargs): # pylint: disable=W1113
CSVableParser.__init__(self, csvAbleClass, encoding)
if handleComments:
csvFile = (line for line in csvFile if not line.strip().startswith(self.COMMENT))
DictReader.__init__(self, csvFile, None if useHeader else self._fieldNames or (), csvAbleClass.READ_REST_KEY, csvAbleClass.READ_REST_VAL, *args, **kwargs)
if useHeader and self.fieldnames and self._fieldNames is None:
self.validateObjectFields(self.fieldnames)
def __init__(self, fid, commentchar='#', *args, **kwds):
if issubclass(DictReader, object):
super(DictReader, self).__init__(fid, *args, **kwds)
else:
DictReader.__init__(self, fid, *args, **kwds)
self.commentchar = commentchar
self.leadingfield = self.commentchar + 'label'
def __init__(self, fid, commentchar='#', *args, **kwds):
if issubclass(DictReader, object):
super(DictReader, self).__init__(fid, *args, **kwds)
else:
DictReader.__init__(self, fid, *args, **kwds)
self.commentchar = commentchar
self.leadingfield = self.commentchar + 'label'
def __init__(self, csvfile, casts, fieldnames=None, restkey=None,
restval=None, dialect='excel', *args, **kwds):
"""Arguments:
- f: An iterable object such as as file. Passed on to
csv.DictReader
- casts: A dict mapping from attribute names to functions to apply
to these names, e.g., {'id':int, 'salary':float}
- fieldnames: Passed on to csv.DictReader
- restkey: Passed on to csv.DictReader
- restval: Passed on to csv.DictReader
- dialect: Passed on to csv.DictReader
- *args: Passed on to csv.DictReader
- **kwds: Passed on to csv.DictReader
"""
DictReader.__init__(self, csvfile, fieldnames=fieldnames,
restkey=restkey, restval=restval, dialect=dialect,
*args, **kwds)
if not type(casts) == dict:
raise TypeError("The casts argument must be a dict")
for v in casts.values():
if not callable(v):
raise TypeError("The values in casts must be callable")
self._casts = casts
def __init__(self, f, fieldnames=None, restkey=None, restval=None,
dialect="excel", *args, **kw):
DictReader.__init__(self, f, fieldnames=fieldnames,
restkey=restkey, restval=restval,
dialect=dialect, *args, **kw)
# Replace the reader with our unicode-enabled reader.
self.reader = UnicodeReader(f, dialect=dialect, *args, **kw)
def __init__(self, affyfn):
'''*affyfn* is either a filename or a file-like object representing a bioconductor output file'''
if isinstance(affyfn, str):
bed = open(bed, 'rU')
DictReader.__init__(self,
bed,
delimiter='\t',
fieldnames=BEDOutput.FIELD_NAMES)
def __init__(self, bed):
'''*bed* is either a filename or a file-like object representing a BED file'''
if isinstance(bed, str):
bed = open(bed, 'rU')
DictReader.__init__(self,
bed,
delimiter='\t',
fieldnames=BEDOutput.FIELD_NAMES)
def __init__(self, *args, **kwargs):
args = list(args)
args[0] = utfify(args[0])
DictReader.__init__(
self, *args,
**kwargs) # DictReader is apparently an old-style class
def __init__(self, f, fieldnames=None, restkey=None, restval=None,
dialect="excel", encoding='utf-8', *args, **kw):
DictReader.__init__(self, f, fieldnames=fieldnames,
restkey=restkey, restval=restval,
dialect=dialect, *args, **kw)
if not encoding is None:
f = Utf8Recoder(f, encoding=encoding)
# Replace the reader with our unicode-enabled reader.
self.reader = reader(f, dialect=dialect, *args, **kw)
def __init__(self, fileobj, fieldnames=None,
key_value_separator=DEFAULT_KEYVALUE_SEPARATOR,
key_value_assigner=DEFAULT_KEYVALUE_ASSIGNER, **kwargs):
kwargs.update(restval=kwargs.get('restval', DEFAULT_RESTVAL),
restkey=kwargs.get('restkey', DEFAULT_RESTKEY),
dialect=kwargs.get('dialect', DEFAULT_DIALECT))
self.fileobj = fileobj
DictReader.__init__(self, fileobj, fieldnames=fieldnames, **kwargs)
self.key_value_separator = key_value_separator
self.key_value_assigner = key_value_assigner
def __init__(self, refGene_fn):
refGene_f = open(refGene_fn, 'rU')
# check for header
first_line = refGene_f.next()
if not first_line.strip().startswith('#'):
refGene_f.seek(0) # first line not header, reset the file pointer
DictReader.__init__(self,
refGene_f,
delimiter='\t',
fieldnames=RefGeneOutput.FIELD_NAMES)
def __init__(self, f, fieldnames=None, restkey=None, restval=None,
dialect="excel",
encoding=None,
*args, **kwds):
BaseDictReader.__init__(self, f=f, fieldnames=fieldnames,
restkey=restkey, restval=restval,
dialect=dialect,
*args, **kwds)
from .csv import reader
self.reader = reader(f, dialect=dialect,
encoding=encoding,
**kwds)
def __init__(self, csvfile, fields=None, silent=False, **kwargs):
self.csvfile = csvfile
self.rows_imported = 0
self.errors = []
self.silent = silent
if fields:
if isinstance(fields[0], (list, tuple)):
kwargs['fieldnames'] = [field[0] for field in fields]
self.field_types = dict(fields)
else:
kwargs['fieldnames'] = fields
self.field_types = dict.fromkeys(fields, None)
DictReader.__init__(self, csvfile, **kwargs)
else:
DictReader.__init__(self, csvfile, **kwargs)
self.field_types = dict.fromkeys(self.fieldnames, None)
def __init__(self,
f,
fieldnames=None,
restkey=None,
restval=None,
dialect="excel",
encoding="utf-8",
*args,
**kwargs):
from csv import DictReader
DictReader.__init__(self, f, fieldnames, restkey, restval, dialect,
*args, **kwargs)
self.reader = UnicodeReader(f,
dialect,
encoding=encoding,
*args,
**kwargs)
def __init__(self,
f,
fieldnames=None,
restkey=None,
restval=None,
dialect="excel",
encoding='utf-8',
*args,
**kw):
DictReader.__init__(self,
f,
fieldnames=fieldnames,
restkey=restkey,
restval=restval,
dialect=dialect,
*args,
**kw)
if not encoding is None:
f = Utf8Recoder(f, encoding=encoding)
# Replace the reader with our unicode-enabled reader.
self.reader = reader(f, dialect=dialect, *args, **kw)
def __init__(self,
csvfile,
fields=None,
silent=False,
allow_json=False,
**kwargs):
self.csvfile = csvfile
self.rows_imported = 0
self.errors = []
self.silent = silent
self.allow_json = allow_json
if fields:
if isinstance(fields[0], (list, tuple)):
kwargs['fieldnames'] = [field[0] for field in fields]
self.field_types = dict(fields)
else:
kwargs['fieldnames'] = fields
self.field_types = dict.fromkeys(fields, None)
DictReader.__init__(self, csvfile, **kwargs)
else:
DictReader.__init__(self, csvfile, **kwargs)
self.field_types = dict.fromkeys(self.fieldnames, None)
def __init__(self, csvfile, casts, fieldnames=None, restkey=None,
restval=None, dialect='excel', *args, **kwds):
"""Arguments:
- f: An iterable object such as as file. Passed on to
csv.DictReader
- casts: A dict mapping from attribute names to functions to apply
to these names, e.g., {'id':int, 'salary':float}
- fieldnames: Passed on to csv.DictReader
- restkey: Passed on to csv.DictReader
- restval: Passed on to csv.DictReader
- dialect: Passed on to csv.DictReader
- *args: Passed on to csv.DictReader
- **kwds: Passed on to csv.DictReader
"""
DictReader.__init__(self, csvfile, fieldnames=fieldnames,
restkey=restkey, restval=restval, dialect=dialect,
*args, **kwds)
if not type(casts) == dict:
raise TypeError("The casts argument must be a dict")
for v in casts.values():
if not callable(v):
raise TypeError("The values in casts must be callable")
self._casts = casts
def __init__(self,affyfn) :
'''*affyfn* is either a filename or a file-like object representing a bioconductor output file'''
if isinstance(affyfn,str) :
bed = open(bed)
DictReader.__init__(self,bed,delimiter='\t',
fieldnames=BEDOutput.FIELD_NAMES)
def __init__(self,bed) :
'''*bed* is either a filename or a file-like object representing a BED file'''
if isinstance(bed,str) :
bed = open(bed)
DictReader.__init__(self,bed,delimiter='\t',
fieldnames=BEDOutput.FIELD_NAMES)
def __init__(self, *args, **kwargs):
args = list(args)
args[0] = utfify(args[0])
DictReader.__init__(self, *args, **kwargs) # DictReader is apparently an old-style class
def __init__(self, f):
DictReader.__init__(self, f)
self._node = Node(ROOT, [])
self.col_num = 0
self._init()
def __init__(self, f, fieldnames=None, restkey=None, restval=None,
dialect="excel", encoding="utf-8", *args, **kwargs):
from csv import DictReader
DictReader.__init__(self, f, fieldnames, restkey, restval,
dialect, *args, **kwargs)
self.reader = UnicodeReader(f, dialect, encoding=encoding, *args, **kwargs)
def __init__(self, caller_cls=None, *args, **kwargs):
DictReader.__init__(self, *args, **kwargs)
self.caller_cls = caller_cls
def __init__(self, *args, **kwargs):
DictReader.__init__(self, *args, **kwargs)
self._fieldnames = map(slugify, self.fieldnames)