Package Bio :: Package Restriction :: Module Restriction :: Class Analysis
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Class Analysis

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         object --+        
                  |        
                set --+    
                      |    
       RestrictionBatch --+
                          |
             object --+   |
                      |   |
PrintFormat.PrintFormat --+
                          |
                         Analysis

Instance Methods [hide private]
new RestrictionBatch.
__init__(self, restrictionbatch=RestrictionBatch([]), sequence=Seq('', Alphabet()), linear=True)
Analysis([restrictionbatch [, sequence] linear=True]) -> New Analysis class.
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__repr__(self)
repr(x)
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dict
_sub_set(A, other_set)
Internal use only.
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tuple
_boundaries(A, start, end)
Format the boundaries for use with the methods that limit the search to only part of the sequence given to analyse.
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bool
_test_normal(A, start, end, site)
Internal use only Test if site is in between start and end.
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bool
_test_reverse(A, start, end, site)
Internal use only Test if site is in between end and start (for circular sequences).
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print the results from dct
print_that(A, dct=..., title=..., s1=...=...)
If dct is not given the full dictionary is used.
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Change attribute of Analysis
change(A, **attribute_name)
It is possible to change the width of the shell by setting self.ConsoleWidth to what you want.
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dict
full(A)
Full Restriction Map of the sequence.
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dict
blunt(A, dct=...)
Only the enzymes which have a 3'overhang restriction site.
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dict
overhang5(A, dct=...)
Only the enzymes which have a 5' overhang restriction site.
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dict
overhang3(A, dct=...)
Only the enzymes which have a 3'overhang restriction site.
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dict
defined(A, dct=...)
Only the enzymes that have a defined restriction site in Rebase.
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dict
with_sites(A, dct=...)
Enzymes which have at least one site in the sequence.
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dict
without_site(A, dct=...)
Enzymes which have no site in the sequence.
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dict
with_N_sites(A, N, dct=...)
Enzymes which cut N times the sequence.
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with_number_list(self, list, dct=None) source code
Limit the search to the enzymes named in list_of_names.
with_name(A, list_of_names, dct=...) source code
Limit the search to the enzymes whose site is of size <site_size>.
with_site_size(A, site_size, dct=...) source code
dict
only_between(A, start, end, dct=...)
Enzymes that cut the sequence only in between start and end.
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dict
between(A, start, end, dct=...)
Enzymes that cut the sequence at least in between start and end.
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dict
show_only_between(A, start, end, dct=...)
Enzymes that cut the sequence outside of the region in between start and end but do not cut inside.
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dict
only_outside(A, start, end, dct=...)
Enzymes that cut the sequence outside of the region in between start and end but do not cut inside.
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outside(self, start, end, dct=None)
A.outside((start, end [, dct]) -> dict.
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dict
do_not_cut(A, start, end, dct=...)
Enzymes that do not cut the region in between start and end.
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Inherited from RestrictionBatch: __add__, __contains__, __div__, __iadd__, __rdiv__, __str__, add, add_nocheck, add_supplier, as_string, current_suppliers, elements, format, get, is_restriction, lambdasplit, remove, search, split

Inherited from set: __and__, __cmp__, __eq__, __ge__, __getattribute__, __gt__, __iand__, __ior__, __isub__, __iter__, __ixor__, __le__, __len__, __lt__, __ne__, __new__, __or__, __rand__, __reduce__, __ror__, __rsub__, __rxor__, __sizeof__, __sub__, __xor__, clear, copy, difference, difference_update, discard, intersection, intersection_update, isdisjoint, issubset, issuperset, pop, symmetric_difference, symmetric_difference_update, union, update

Inherited from PrintFormat.PrintFormat: make_format, print_as

Inherited from object: __delattr__, __format__, __reduce_ex__, __setattr__, __subclasshook__

Class Methods [hide private]

Inherited from RestrictionBatch: show_codes, suppl_codes

Class Variables [hide private]

Inherited from set: __hash__

Inherited from PrintFormat.PrintFormat: Cmodulo, ConsoleWidth, Indent, MaxSize, NameWidth, PrefWidth, linesize

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, restrictionbatch=RestrictionBatch([]), sequence=Seq('', Alphabet()), linear=True)
(Constructor)

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Analysis([restrictionbatch [, sequence] linear=True]) -> New Analysis class.

For most of the method of this class if a dictionary is given it will be used as the base to calculate the results. If no dictionary is given a new analysis using the Restriction Batch which has been given when the Analysis class has been instantiated.

Returns: new RestrictionBatch.
Overrides: object.__init__

__repr__(self)
(Representation operator)

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repr(x)

Overrides: object.__repr__
(inherited documentation)

_sub_set(A, other_set)

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Internal use only.

screen the results through wanted set. Keep only the results for which the enzymes is in wanted set.

Returns: dict

print_that(A, dct=..., title=..., s1=...=...)

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If dct is not given the full dictionary is used.
Returns: print the results from dct
Overrides: PrintFormat.PrintFormat.print_that

change(A, **attribute_name)

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It is possible to change the width of the shell by setting self.ConsoleWidth to what you want. self.NameWidth refer to the maximal length of the enzyme name.

Changing one of these parameters here might not give the results you expect. In which case, you can settle back to a 80 columns shell or try to change self.Cmodulo and self.PrefWidth in PrintFormat until you get it right.

Returns: Change attribute of Analysis

between(A, start, end, dct=...)

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Enzymes that cut the sequence at least in between start and end. They may cut outside as well.
Returns: dict

outside(self, start, end, dct=None)

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A.outside((start, end [, dct]) -> dict.

Enzymes that cut outside the region in between start and end. No test is made to know if they cut or not inside this region.