def _swap_query_and_sbjct(self):
"""
USE WITH CARE!!!
Swap query and sbjct sequences and positions.
This enables easier comparison in some cases.
It is done WITHIN THIS INITIALIZED object.
That is what I mean with use with care.
Recommended usage is only with the helper function
``swap_query_and_sbjct``
Usage:
``swapped_pacb = swap_query_and_sbjct(pacb)``
"""
# first swap the data from the basal PacbP clas
PacbP._swap_query_and_sbjct(self)
# swap strings and orf objects
self.query_dna, self.sbjct_dna = self.sbjct_dna, self.query_dna
# swap coordinates
(a,b,c) = (self.query_dna_start, self.query_dna_end, self.query_dna_length)
(d,e,f) = (self.sbjct_dna_start, self.sbjct_dna_end, self.sbjct_dna_length)
(self.query_dna_start, self.query_dna_end, self.query_dna_length) = (d,e,f)
(self.sbjct_dna_start, self.sbjct_dna_end, self.sbjct_dna_length) = (a,b,c)
# and swap the alignment on all positions
for adp_pos in self._positions:
adp_pos._swap_query_and_sbjct()
def _strip_one_left_position(self):
"""
"""
# no truncation possible -> PacbP does not exist anymore
if self.length == 0: raise ZeroSizedPacb
if self.query[0] != "-":
self.query_dna = self.query_dna[3:]
self.query_dna_start = self.query_dna_start+3
self.query_dna_length = self.query_dna_length-3
if self.sbjct[0] != "-":
self.sbjct_dna = self.sbjct_dna[3:]
self.sbjct_dna_start = self.sbjct_dna_start+3
self.sbjct_dna_length = self.sbjct_dna_length-3
# increase `position` counter for all existing positions
for pos in self._positions: pos.position-=1
# and pop leading aligned position
self._positions.pop(0)
# COMPENSATE self._original_alignment_pos_start and end
if self._original_alignment_pos_start > 0:
self._original_alignment_pos_start-=1
self._original_alignment_pos_end-=1
elif self._original_alignment_pos_start==0:
self._original_alignment_pos_end-=1
else:
raise "WHATEVER; coords for original alignment not oke"
# correct all the protein coordinates and strings
PacbP._strip_one_left_position(self)
def _strip_one_rigth_position(self):
"""
"""
# no truncation possible -> PacbP does not exist anymore
if self.length == 0: raise ZeroSizedPacb
if self.query[-1] != "-":
self.query_dna = self.query_dna[0:-3]
self.query_dna_end = self.query_dna_end-3
self.query_dna_length = self.query_dna_length-3
if self.sbjct[-1] != "-":
self.sbjct_dna = self.sbjct_dna[0:-3]
self.sbjct_dna_end = self.sbjct_dna_end-3
self.sbjct_dna_length = self.sbjct_dna_length-3
# COMPENSATE self._original_alignment_pos_end
if len(self._positions) == self._original_alignment_pos_end:
self._original_alignment_pos_end-=1
elif len(self._positions) > self._original_alignment_pos_end:
pass
else:
raise "WHATEVER; coords for original alignment not oke"
# and pop trailing aligned position
self._positions.pop()
# correct all the protein coordinates and strings
PacbP._strip_one_rigth_position(self)
def _swap_query_and_sbjct(self):
"""
USE WITH CARE!!!
Swap query and sbjct sequences and positions.
This enables easier comparison in some cases.
It is done WITHIN THIS INITIALIZED object.
That is what I mean with use with care.
Recommended usage is only with the helper function
``swap_query_and_sbjct``
Usage:
``swapped_pacb = swap_query_and_sbjct(pacb)``
"""
# first swap the data from the basal PacbP clas
PacbP._swap_query_and_sbjct(self)
# swap strings and orf objects
self.query_dna, self.sbjct_dna = self.sbjct_dna, self.query_dna
# swap coordinates
(a, b, c) = (self.query_dna_start, self.query_dna_end,
self.query_dna_length)
(d, e, f) = (self.sbjct_dna_start, self.sbjct_dna_end,
self.sbjct_dna_length)
(self.query_dna_start, self.query_dna_end,
self.query_dna_length) = (d, e, f)
(self.sbjct_dna_start, self.sbjct_dna_end,
self.sbjct_dna_length) = (a, b, c)
# and swap the alignment on all positions
for adp_pos in self._positions:
adp_pos._swap_query_and_sbjct()
def _strip_one_rigth_position(self):
"""
"""
# no truncation possible -> PacbP does not exist anymore
if self.length == 0: raise ZeroSizedPacb
if self.query[-1] != "-":
self.query_dna = self.query_dna[0:-3]
self.query_dna_end = self.query_dna_end - 3
self.query_dna_length = self.query_dna_length - 3
if self.sbjct[-1] != "-":
self.sbjct_dna = self.sbjct_dna[0:-3]
self.sbjct_dna_end = self.sbjct_dna_end - 3
self.sbjct_dna_length = self.sbjct_dna_length - 3
# COMPENSATE self._original_alignment_pos_end
if len(self._positions) == self._original_alignment_pos_end:
self._original_alignment_pos_end -= 1
elif len(self._positions) > self._original_alignment_pos_end:
pass
else:
raise "WHATEVER; coords for original alignment not oke"
# and pop trailing aligned position
self._positions.pop()
# correct all the protein coordinates and strings
PacbP._strip_one_rigth_position(self)
def _strip_one_left_position(self):
"""
"""
# no truncation possible -> PacbP does not exist anymore
if self.length == 0: raise ZeroSizedPacb
if self.query[0] != "-":
self.query_dna = self.query_dna[3:]
self.query_dna_start = self.query_dna_start + 3
self.query_dna_length = self.query_dna_length - 3
if self.sbjct[0] != "-":
self.sbjct_dna = self.sbjct_dna[3:]
self.sbjct_dna_start = self.sbjct_dna_start + 3
self.sbjct_dna_length = self.sbjct_dna_length - 3
# increase `position` counter for all existing positions
for pos in self._positions:
pos.position -= 1
# and pop leading aligned position
self._positions.pop(0)
# COMPENSATE self._original_alignment_pos_start and end
if self._original_alignment_pos_start > 0:
self._original_alignment_pos_start -= 1
self._original_alignment_pos_end -= 1
elif self._original_alignment_pos_start == 0:
self._original_alignment_pos_end -= 1
else:
raise "WHATEVER; coords for original alignment not oke"
# correct all the protein coordinates and strings
PacbP._strip_one_left_position(self)
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)