def __init__(self,
input=("", "", 0, 0),
blastp_hsp=None,
MATRIX=None,
gff={}):
""" """
PacbP.__init__(self,
input=input,
blastp_hsp=blastp_hsp,
MATRIX=MATRIX,
gff=gff)
def __init__(self,
input=("", "", 0, 0),
blastp_hsp=None,
MATRIX={},
pacbp=None,
input_dna=("", "", 0, 0)):
"""
"""
# first, get to the point of an instantiated PacbP object
if str(pacbp.__class__) in ['pacb.PacbP', 'pacb.pacbp.PacbP']:
# loop over all attributes, and copy all true attributes
# skip the `__`-starting attributes and the `instancemethods`
for attr in dir(pacbp):
if attr[0:2] == "__": continue
if str(type(getattr(pacbp,
attr))) != "<type 'instancemethod'>":
# copy this attribute from PacbP to PacbPDNA
setattr(self, attr, getattr(pacbp, attr))
# and move the original hsp object
self._hsp = pacbp._hsp
# check if a non-default matrix was applied
if MATRIX:
self.MATRIX = MATRIX
else:
# call the __init__ function of the basal PacbP class
if MATRIX:
PacbP.__init__(self,
input=input,
blastp_hsp=blastp_hsp,
MATRIX=MATRIX)
else:
PacbP.__init__(self, input=input, blastp_hsp=blastp_hsp)
# set the PacbPDNA specific attributes
self.query_dna = ""
self.query_dna_start = 0
self.query_dna_end = 0
self.query_dna_length = 0
self.sbjct_dna = ""
self.sbjct_dna_start = 0
self.sbjct_dna_end = 0
self.sbjct_dna_length = 0
self._positions = []
# and finish initialization
self._initialize(input_dna)
self._alignment2positions()
# set start and end positions of the original alignment
# this is needed to calculate the `entropy` of a position
# in the alignment
self._original_alignment_pos_start = 0
self._original_alignment_pos_end = len(self._positions)
def __init__(self,input=("","",0,0),blastp_hsp=None,MATRIX={},
pacbp=None,input_dna=("","",0,0)):
"""
"""
# first, get to the point of an instantiated PacbP object
if str(pacbp.__class__) in ['pacb.PacbP','pacb.pacbp.PacbP']:
# loop over all attributes, and copy all true attributes
# skip the `__`-starting attributes and the `instancemethods`
for attr in dir(pacbp):
if attr[0:2] == "__": continue
if str(type(getattr(pacbp,attr))) != "<type 'instancemethod'>":
# copy this attribute from PacbP to PacbPDNA
setattr(self,attr,getattr(pacbp,attr))
# and move the original hsp object
self._hsp = pacbp._hsp
# check if a non-default matrix was applied
if MATRIX:
self.MATRIX = MATRIX
else:
# call the __init__ function of the basal PacbP class
if MATRIX:
PacbP.__init__(self,input=input,blastp_hsp=blastp_hsp,MATRIX=MATRIX)
else:
PacbP.__init__(self,input=input,blastp_hsp=blastp_hsp)
# set the PacbPDNA specific attributes
self.query_dna = ""
self.query_dna_start = 0
self.query_dna_end = 0
self.query_dna_length = 0
self.sbjct_dna = ""
self.sbjct_dna_start = 0
self.sbjct_dna_end = 0
self.sbjct_dna_length = 0
self._positions = []
# and finish initialization
self._initialize(input_dna)
self._alignment2positions()
# set start and end positions of the original alignment
# this is needed to calculate the `entropy` of a position
# in the alignment
self._original_alignment_pos_start = 0
self._original_alignment_pos_end = len(self._positions)
def __init__(self,input=("","",0,0),blastp_hsp=None,MATRIX=None,gff={}):
""" """
PacbP.__init__(self,input=input,blastp_hsp=blastp_hsp,MATRIX=MATRIX,gff=gff)
