def __init__(
self,
start,
end,
strand="+",
score=".",
frame=".",
fref=None,
fsource=None,
fmethod=None,
attribute_string="",
gff={},
):
"""
@type start: number
@param start: start coord of Feature in PYTHON COORDINATE (GFF-1)
@type end: number
@param end: end coord of Feature
@type strand: string
@param strand: ['+','-','.'] or None, default '+'
@type score: float
@param score: score of Feature, default "."
@type frame: number
@param frame: [0,1,2,'.'] or None, default "."
@type phase: USE FRAME IN STEAD OF PHASE
@param phase: USE FRAME IN STEAD OF PHASE
@type fref: string
@param fref: default None ('None'), to be set lateron with seqname
@type fsource: string
@param fsource: default None ('None'), mostly inherited
@type fmethod: string
@param fmethod: default None ('None'), mostly inherited
@type gff: dictionary
@param gff: dictionary with (default) gff data. Possible keys are:
'fref', 'fmethod', 'fstrand', 'fsource', 'gclass', 'gname'
@attention: TODO gff dictionary application is not coded yet!
"""
if fsource == None:
fsource = self.__class__.__name__
if fmethod == None:
fmethod = self.__class__.__name__
gfflist = [fref, fsource, fmethod, start, end, score, strand, frame]
PythonGffFeature.__init__(self, "\t".join([str(elem) for elem in gfflist]))
def __init__(self,
start,
end,
strand="+",
score=".",
frame=".",
fref=None,
fsource=None,
fmethod=None,
attribute_string="",
gff={}):
"""
@type start: number
@param start: start coord of Feature in PYTHON COORDINATE (GFF-1)
@type end: number
@param end: end coord of Feature
@type strand: string
@param strand: ['+','-','.'] or None, default '+'
@type score: float
@param score: score of Feature, default "."
@type frame: number
@param frame: [0,1,2,'.'] or None, default "."
@type phase: USE FRAME IN STEAD OF PHASE
@param phase: USE FRAME IN STEAD OF PHASE
@type fref: string
@param fref: default None ('None'), to be set lateron with seqname
@type fsource: string
@param fsource: default None ('None'), mostly inherited
@type fmethod: string
@param fmethod: default None ('None'), mostly inherited
@type gff: dictionary
@param gff: dictionary with (default) gff data. Possible keys are:
'fref', 'fmethod', 'fstrand', 'fsource', 'gclass', 'gname'
@attention: TODO gff dictionary application is not coded yet!
"""
if fsource == None: fsource = self.__class__.__name__
if fmethod == None: fmethod = self.__class__.__name__
gfflist = [fref, fsource, fmethod, start, end, score, strand, frame]
PythonGffFeature.__init__(self,
"\t".join([str(elem) for elem in gfflist]))
def togff(self):
""" Original __str__ function of Pyhtongff.gff.feature.Feature """
if not self.gclass():
self.gclass(self.__class__.__name__)
if not self.gname():
self.gname(str(self.start() + 1))
return PythonGffFeature.__str__(self)
def togff(self):
""" Original __str__ function of Pyhtongff.gff.feature.Feature """
if not self.gclass(): self.gclass(self.__class__.__name__)
if not self.gname(): self.gname(str(self.start() + 1))
return PythonGffFeature.__str__(self)