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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 70 | 2 | 6 | 0.951 | block |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 80 | 512 | Bio/Restriction/Restriction.py |
| 2 | 70 | 593 | Bio/Restriction/Restriction.py |
| ||||
"""Implement the methods specific to the enzymes that do not cut.
These enzymes are generally enzymes that have been only partially
characterised and the way they cut the DNA is unknow or enzymes for
which the pattern of cut is to complex to be recorded in Rebase
(ncuts values of 0 in emboss_e.###).
When using search() with these enzymes the values returned are at the start of
the restriction site.
Their catalyse() method returns a TypeError.
Unknown and NotDefined are also part of the base classes of these enzymes.
Internal use only. Not meant to be instantiated."""
def cut_once(self):
"""RE.cut_once() -> bool.
True if the enzyme cut the sequence one time on each strand."""
return False
cut_once = classmethod(cut_once)
def cut_twice(self):
"""RE.cut_twice() -> bool.
True if the enzyme cut the sequence twice on each strand."""
return False
cut_twice = classmethod(cut_twice)
def _modify(self,location):
"""RE._modify(location) -> int.
for internal use only.
location is an integer corresponding to the location of the match for
the enzyme pattern in the sequence.
_modify returns the real place where the enzyme will cut.
example :
EcoRI pattern : GAATTC
EcoRI will cut after the G.
so in the sequence :
______
GAATACACGGAATTCGA
|
10
dna.finditer(GAATTC, 6) will return 10 as G is the 10th base
EcoRI cut after the G so :
EcoRI._modify(10) -> 11.
if the enzyme cut twice _modify will returns two integer corresponding
to each cutting site.
"""
yield location
_modify = classmethod(_modify)
def _rev_modify(self,location):
"""RE._rev_modify(location) -> generator of int.
for internal use only.
as _modify for site situated on the antiparallel strand when the
enzyme is not palindromic
"""
yield location
_rev_modify = classmethod(_rev_modify)
def characteristic(self):
"""RE.characteristic() -> tuple.
the tuple contains the attributes :
fst5 -> first 5' cut ((current strand) or None
fst3 -> first 3' cut (complementary strand) or None
scd5 -> second 5' cut (current strand) or None
scd5 -> second 3' cut (complementary strand) or None
site -> recognition site."""
return None,None,None,None,self.site
characteristic = classmethod(characteristic)
|
| ||||
"""Implement the methods specific to the enzymes that cut the DNA only once
Correspond to ncuts values of 2 in emboss_e.###
Internal use only. Not meant to be instantiated."""
def cut_once(self):
"""RE.cut_once() -> bool.
True if the enzyme cut the sequence one time on each strand."""
return True
cut_once = classmethod(cut_once)
def cut_twice(self):
"""RE.cut_twice() -> bool.
True if the enzyme cut the sequence twice on each strand."""
return False
cut_twice = classmethod(cut_twice)
def _modify(self,location):
"""RE._modify(location) -> int.
for internal use only.
location is an integer corresponding to the location of the match for
the enzyme pattern in the sequence.
_modify returns the real place where the enzyme will cut.
example :
EcoRI pattern : GAATTC
EcoRI will cut after the G.
so in the sequence :
______
GAATACACGGAATTCGA
|
10
dna.finditer(GAATTC, 6) will return 10 as G is the 10th base
EcoRI cut after the G so :
EcoRI._modify(10) -> 11.
if the enzyme cut twice _modify will returns two integer corresponding
to each cutting site.
"""
yield location+self.fst5
_modify = classmethod(_modify)
def _rev_modify(self,location):
"""RE._rev_modify(location) -> generator of int.
for internal use only.
as _modify for site situated on the antiparallel strand when the
enzyme is not palindromic
"""
yield location-self.fst3
_rev_modify = classmethod(_rev_modify)
def characteristic(self):
"""RE.characteristic() -> tuple.
the tuple contains the attributes :
fst5 -> first 5' cut ((current strand) or None
fst3 -> first 3' cut (complementary strand) or None
scd5 -> second 5' cut (current strand) or None
scd5 -> second 3' cut (complementary strand) or None
site -> recognition site."""
return self.fst5,self.fst3,None,None,self.site
characteristic = classmethod(characteristic)
|
| |||
[[#variable1a3dfe20]]
def cut_once(self):
"""RE.cut_once() -> bool.
True if the enzyme cut the sequence one time on each strand."""
return [[#variable5e537ac0]]
cut_once = classmethod(cut_once)
def cut_twice(self):
"""RE.cut_twice() -> bool.
True if the enzyme cut the sequence twice on each strand."""
return False
cut_twice = classmethod(cut_twice)
def _modify(self,location):
"""RE._modify(location) -> int.
for internal use only.
location is an integer corresponding to the location of the match for
the enzyme pattern in the sequence.
_modify returns the real place where the enzyme will cut.
example :
EcoRI pattern : GAATTC
EcoRI will cut after the G.
so in the sequence :
______
GAATACACGGAATTCGA
|
10
dna.finditer(GAATTC, 6) will return 10 as G is the 10th base
EcoRI cut after the G so :
EcoRI._modify(10) -> 11.
if the enzyme cut twice _modify will returns two integer corresponding
to each cutting site.
"""
yield [[#variable5e537b00]]
_modify = classmethod(_modify)
def _rev_modify(self,location):
"""RE._rev_modify(location) -> generator of int.
for internal use only.
as _modify for site situated on the antiparallel strand when the
enzyme is not palindromic
"""
yield [[#variable2cdc32a0]]
_rev_modify = classmethod(_rev_modify)
def characteristic(self):
"""RE.characteristic() -> tuple.
the tuple contains the attributes :
fst5 -> first 5' cut ((current strand) or None
fst3 -> first 3' cut (complementary strand) or None
scd5 -> second 5' cut (current strand) or None
scd5 -> second 3' cut (complementary strand) or None
site -> recognition site."""
return [[#variable2dc28480]], [[#variable1a3dfea0]],None,None,self.site
characteristic = classmethod(characteristic)
|
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#1a3dfe20]] | """Implement the methods specific to the enzymes that cut the DNA only once
Correspond to ncuts values of 2 in emboss_e.###
Internal use only. Not meant to be instantiated.""" |
| 1 | 2 | [[#1a3dfe20]] | """Implement the methods specific to the enzymes that do not cut.
These enzymes are generally enzymes that have been only partially
characterised and the way they cut the DNA is unknow or enzymes for
which the pattern of cut is to complex to be recorded in Rebase
(ncuts values of 0 in emboss_e.###).
When using search() with these enzymes the values returned are at the start of
the restriction site.
Their catalyse() method returns a TypeError.
Unknown and NotDefined are also part of the base classes of these enzymes.
Internal use only. Not meant to be instantiated.""" |
| 2 | 1 | [[#5e537ac0]] | True |
| 2 | 2 | [[#5e537ac0]] | False |
| 3 | 1 | [[#5e537b00]] | location+self.fst5 |
| 3 | 2 | [[#5e537b00]] | location |
| 4 | 1 | [[#2cdc32a0]] | location-self.fst3 |
| 4 | 2 | [[#2cdc32a0]] | location |
| 5 | 1 | [[#2dc28480]] | self.fst5 |
| 5 | 2 | [[#2dc28480]] | None |
| 6 | 1 | [[#1a3dfea0]] | self.fst3 |
| 6 | 2 | [[#1a3dfea0]] | None |