CloneSet103


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[Sequence Length]
70260.951block
Clone AbstractionParameter Bindings
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Line CountSource Line
Source File
180512
Bio/Restriction/Restriction.py
270593
Bio/Restriction/Restriction.py
Clone Instance
1
Line Count
80
Source Line
512
Source File
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) 


Clone Instance
2
Line Count
70
Source Line
593
Source File
Bio/Restriction/Restriction.py

    """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) 


Clone AbstractionParameter Count: 6Parameter Bindings

   [[#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 Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#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.""" 
12[[#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.""" 
21[[#5e537ac0]]
True 
22[[#5e537ac0]]
False 
31[[#5e537b00]]
location+self.fst5 
32[[#5e537b00]]
location 
41[[#2cdc32a0]]
location-self.fst3 
42[[#2cdc32a0]]
location 
51[[#2dc28480]]
self.fst5 
52[[#2dc28480]]
None 
61[[#1a3dfea0]]
self.fst3 
62[[#1a3dfea0]]
None