Package Bio :: Package Restriction :: Module Restriction :: Class Ambiguous
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Type Ambiguous

source code

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

Implement the methods specific to the enzymes for which the overhang
is variable.

Typical example : BstXI -> CCAN_NNNN^NTGG
                  The overhang can be any sequence of 4 bases.
Notes:
    Blunt enzymes are always defined. even if there site is GGATCCNNN^_N
    There overhang is always the same : blunt!

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__, __instancecheck__, __new__, __setattr__, __subclasscheck__, __subclasses__, mro

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

Class Methods [hide private]
list

_drop(RE)
for internal use only.
source code
bool

is_defined(RE)
True if the sequence recognised and cut is constant, i.e.
source code
bool

is_ambiguous(RE)
True if the sequence recognised and cut is ambiguous, i.e.
source code
bool

is_unknown(RE)
True if the sequence is unknown, i.e.
source code
bool

_mod2(RE, other)
for internal use only
source code
str

elucidate(RE)
return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'.
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__, __itemsize__, __mro__, __name__, __weakrefoffset__

Inherited from object: __class__

Method Details [hide private]

_drop(RE)
Class Method

source code 
for internal use only.

drop the site that are situated outside the sequence in linear sequence.
modify the index for site in circular sequences.

Returns:
list

is_defined(RE)
Class Method

source code 
True if the sequence recognised and cut is constant,
i.e. the recognition site is not degenerated AND the enzyme cut inside
the site.

see also:
    RE.is_ambiguous()
    RE.is_unknown()

Returns:
bool

is_ambiguous(RE)
Class Method

source code 
True if the sequence recognised and cut is ambiguous,
i.e. the recognition site is degenerated AND/OR the enzyme cut outside
the site.

see also:
    RE.is_defined()
    RE.is_unknown()

Returns:
bool

is_unknown(RE)
Class Method

source code 
True if the sequence is unknown,
i.e. the recognition site has not been characterised yet.

see also:
    RE.is_defined()
    RE.is_ambiguous()

Returns:
bool

_mod2(RE, other)
Class Method

source code 
for internal use only

test for the compatibility of restriction ending of RE and other.

Returns:
bool

elucidate(RE)
Class Method

source code 
return a representation of the site with the cut on the (+) strand
represented as '^' and the cut on the (-) strand as '_'.
ie:
>>> EcoRI.elucidate()   # 5' overhang
'G^AATT_C'
>>> KpnI.elucidate()    # 3' overhang
'G_GTAC^C'
>>> EcoRV.elucidate()   # blunt
'GAT^_ATC'
>>> SnaI.elucidate()     # NotDefined, cut profile unknown.
'? GTATAC ?'
>>>

Returns:
str