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removed _ovhg property from dseq
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@BjornFJohansson
BjornFJohansson committed Jul 5, 2023
1 parent 2466cc0 commit 30fcb48
Showing 1 changed file with 46 additions and 33 deletions.
79 changes: 46 additions & 33 deletions src/pydna/dseq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -374,7 +374,7 @@ def __init__(
self.watson = _pretty_str(watson)
self.crick = _pretty_str(crick)
self.length = len(self._data)
self._ovhg = ovhg
self.ovhg = ovhg
self.pos = pos

@classmethod
Expand All @@ -390,7 +390,7 @@ def quick(
obj = cls.__new__(cls) # Does not call __init__
obj.watson = _pretty_str(watson)
obj.crick = _pretty_str(crick)
obj._ovhg = ovhg
obj.ovhg = ovhg
obj.circular = circular
# obj._linear = linear
obj.length = max(len(watson) + max(0, ovhg), len(crick) + max(0, -ovhg))
Expand All @@ -412,7 +412,7 @@ def from_string(
obj = cls.__new__(cls) # Does not call __init__
obj.watson = _pretty_str(dna)
obj.crick = _pretty_str(_rc(dna))
obj._ovhg = 0
obj.ovhg = 0
obj.circular = circular
# obj._linear = linear
obj.length = len(dna)
Expand All @@ -424,7 +424,7 @@ def from_string(
def from_representation(cls, dsdna: str, *args, **kwargs):
obj = cls.__new__(cls) # Does not call __init__
w, c, *r = [ln for ln in dsdna.splitlines() if ln]
ovhg = obj._ovhg = len(w) - len(w.lstrip()) - (len(c) - len(c.lstrip()))
ovhg = obj.ovhg = len(w) - len(w.lstrip()) - (len(c) - len(c.lstrip()))
watson = obj.watson = _pretty_str(w.strip())
crick = obj.crick = _pretty_str(c.strip()[::-1])
obj.circular = False
Expand All @@ -436,12 +436,12 @@ def from_representation(cls, dsdna: str, *args, **kwargs):
obj._data = _rc(cb[-max(0, ovhg) or len(cb) :]) + wb + _rc(cb[: max(0, len(cb) - ovhg - len(wb))])
return obj

@property
def ovhg(self):
"""The ovhg property. This cannot be set directly, but is a
consequence of how the watson and crick strands anneal to
each other"""
return self._ovhg
# @property
# def ovhg(self):
# """The ovhg property. This cannot be set directly, but is a
# consequence of how the watson and crick strands anneal to
# each other"""
# return self._ovhg

# @property
# def linear(self):
Expand Down Expand Up @@ -587,10 +587,10 @@ def __getitem__(self, sl):
"""Returns a subsequence. This method is used by the slice notation"""

if not self.circular:
x = len(self.crick) - self._ovhg - len(self.watson)
x = len(self.crick) - self.ovhg - len(self.watson)

sns = (self._ovhg * " " + self.watson + x * " ")[sl]
asn = (-self._ovhg * " " + self.crick[::-1] + -x * " ")[sl]
sns = (self.ovhg * " " + self.watson + x * " ")[sl]
asn = (-self.ovhg * " " + self.crick[::-1] + -x * " ")[sl]

ovhg = max((len(sns) - len(sns.lstrip()), -len(asn) + len(asn.lstrip())), key=abs)

Expand Down Expand Up @@ -634,7 +634,7 @@ def __eq__(self, other):
same = (
other.watson.lower() == self.watson.lower()
and other.crick.lower() == self.crick.lower()
and other.ovhg == self._ovhg
and other.ovhg == self.ovhg
and self.circular == other.circular
)
# Also test for alphabet ?
Expand All @@ -647,15 +647,15 @@ def __repr__(self):
longer than 30 bp"""

if len(self) > Dseq.trunc:
if self._ovhg > 0:
d = self.crick[-self._ovhg :][::-1]
if self.ovhg > 0:
d = self.crick[-self.ovhg :][::-1]
hej = len(d)
if len(d) > 10:
d = "{}..{}".format(d[:4], d[-4:])
a = len(d) * " "

elif self._ovhg < 0:
a = self.watson[: max(0, -self._ovhg)]
elif self.ovhg < 0:
a = self.watson[: max(0, -self.ovhg)]
hej = len(a)
if len(a) > 10:
a = "{}..{}".format(a[:4], a[-4:])
Expand All @@ -665,10 +665,10 @@ def __repr__(self):
d = ""
hej = 0

x = self._ovhg + len(self.watson) - len(self.crick)
x = self.ovhg + len(self.watson) - len(self.crick)

if x > 0:
c = self.watson[len(self.crick) - self._ovhg :]
c = self.watson[len(self.crick) - self.ovhg :]
y = len(c)
if len(c) > 10:
c = "{}..{}".format(c[:4], c[-4:])
Expand All @@ -685,7 +685,7 @@ def __repr__(self):
y = 0

L = len(self) - hej - y
x1 = -min(0, self._ovhg)
x1 = -min(0, self.ovhg)
x2 = x1 + L
x3 = -min(0, x)
x4 = x3 + L
Expand Down Expand Up @@ -715,8 +715,8 @@ def __repr__(self):
self.__class__.__name__,
{False: "-", True: "o"}[self.circular],
len(self),
self._ovhg * " " + self.watson,
-self._ovhg * " " + self.crick[::-1],
self.ovhg * " " + self.watson,
-self.ovhg * " " + self.crick[::-1],
)
)

Expand All @@ -741,7 +741,7 @@ def reverse_complement(self, inplace=False):
>>>
"""
ovhg = len(self.watson) - len(self.crick) + self._ovhg
ovhg = len(self.watson) - len(self.crick) + self.ovhg
return Dseq.quick(
self.crick,
self.watson,
Expand Down Expand Up @@ -809,7 +809,7 @@ def looped(self):
if type5 == type3 and str(sticky5) == str(_rc(sticky3)):
nseq = Dseq.quick(
self.watson,
self.crick[-self._ovhg :] + self.crick[: -self._ovhg],
self.crick[-self.ovhg :] + self.crick[: -self.ovhg],
ovhg=0,
# linear=False,
circular=True,
Expand Down Expand Up @@ -894,11 +894,11 @@ def five_prime_end(self):
return "5'", self.watson.lower()
if not self.watson and self.crick:
return "3'", self.crick.lower()
if self._ovhg < 0:
sticky = self.watson[: -self._ovhg].lower()
if self.ovhg < 0:
sticky = self.watson[: -self.ovhg].lower()
type_ = "5'"
elif self._ovhg > 0:
sticky = self.crick[-self._ovhg :].lower()
elif self.ovhg > 0:
sticky = self.crick[-self.ovhg :].lower()
type_ = "3'"
else:
sticky = ""
Expand Down Expand Up @@ -939,7 +939,7 @@ def three_prime_end(self):
"""

ovhg = len(self.watson) - len(self.crick) + self._ovhg
ovhg = len(self.watson) - len(self.crick) + self.ovhg

if ovhg < 0:
sticky = self.crick[:-ovhg].lower()
Expand Down Expand Up @@ -983,7 +983,7 @@ def __add__(self, other):
other_type, other_tail = other.five_prime_end()

if self_type == other_type and str(self_tail) == str(_rc(other_tail)):
answer = Dseq.quick(self.watson + other.watson, other.crick + self.crick, self._ovhg)
answer = Dseq.quick(self.watson + other.watson, other.crick + self.crick, self.ovhg)
elif not self:
answer = _copy.copy(other)
elif not other:
Expand Down Expand Up @@ -1011,7 +1011,7 @@ def _fill_in_five_prime(self, nucleotides):
stuffer += n
else:
break
return self.crick + stuffer, self._ovhg + len(stuffer)
return self.crick + stuffer, self.ovhg + len(stuffer)

def _fill_in_three_prime(self, nucleotides):
stuffer = ""
Expand Down Expand Up @@ -1218,6 +1218,19 @@ def T4(self, nucleotides=None):

t4 = T4 # alias for the T4 method.

def exo1_front(self, n=1):
"""5'-3' resection at the start (left side) of the molecule."""
d = _copy.deepcopy(self)
d.ovhg += n
d.watson = d.watson[n:]
return d

def exo1_end(self, n=1):
"""5'-3' resection at the end (right side) of the molecule."""
d = _copy.deepcopy(self)
d.crick = d.crick[n:]
return d

def no_cutters(self, batch: _RestrictionBatch = None):
"""Enzymes in a RestrictionBatch not cutting sequence."""
if not batch:
Expand Down Expand Up @@ -1307,7 +1320,7 @@ def isblunt(self):
>>> a.isblunt()
False
"""
return self._ovhg == 0 and len(self.watson) == len(self.crick) and not self.circular
return self.ovhg == 0 and len(self.watson) == len(self.crick) and not self.circular

def cas9(self, RNA: str):
"""docstring."""
Expand Down

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