Package Bio :: Package Restriction :: Module Restriction :: Class TwoCuts
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Type TwoCuts

source code

 object --+            
          |            
       type --+        
              |        
RestrictionType --+    
                  |    
        AbstractCut --+
                      |
                     TwoCuts
Known Subclasses:

Implement the methods specific to the enzymes that cut the DNA twice

Correspond to ncuts values of 4 in emboss_e.###

Internal use only. Not meant to be instantiated.

Instance Methods [hide private]

Inherited from RestrictionType: __add__, __div__, __eq__, __floordiv__, __ge__, __gt__, __hash__, __init__, __le__, __len__, __lt__, __mod__, __ne__, __rdiv__, __repr__, __rfloordiv__, __rshift__, __rtruediv__, __str__, __truediv__

Inherited from type: __call__, __delattr__, __getattribute__, __new__, __setattr__, __subclasses__, mro

Inherited from object: __format__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Class Methods [hide private]
bool
cut_once(RE)
True if the enzyme cut the sequence one time on each strand.
source code
bool
cut_twice(RE)
True if the enzyme cut the sequence twice on each strand.
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int
_modify(RE, location)
for internal use only.
source code
generator of int
_rev_modify(RE, location)
for internal use only.
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tuple
characteristic(RE)
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.
source code

Inherited from AbstractCut: all_suppliers, equischizomers, frequency, is_equischizomer, is_isoschizomer, is_neoschizomer, isoschizomers, neoschizomers, search

Properties [hide private]

Inherited from type: __abstractmethods__, __base__, __bases__, __basicsize__, __dictoffset__, __flags__, __instancecheck__, __itemsize__, __mro__, __name__, __subclasscheck__, __weakrefoffset__

Inherited from object: __class__

Method Details [hide private]

_modify(RE, location)
Class Method

source code 

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.

Returns: int

_rev_modify(RE, location)
Class Method

source code 

for internal use only.

as _modify for site situated on the antiparallel strand when the enzyme is not palindromic

Returns: generator of int