new RestrictionBatch.
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__init__(self,
restrictionbatch=RestrictionBatch(),
sequence=DNA(''),
linear=True)
Analysis([restrictionbatch [, sequence] linear=True]) -> New
Analysis class. |
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dict
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tuple
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_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
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_test_normal(A,
start,
end,
site)
Internal use only Test if site is in between start and end. |
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bool
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_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
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print_that(A,
dct=...,
title=...,
s1=...=...)
If dct is not given the full dictionary is used. |
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Change attribute of Analysis
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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
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full(A)
Full Restriction Map of the sequence. |
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dict
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blunt(A,
dct=...)
Only the enzymes which have a 3'overhang restriction site. |
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dict
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overhang5(A,
dct=...)
Only the enzymes which have a 5' overhang restriction site. |
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dict
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overhang3(A,
dct=...)
Only the enzymes which have a 3'overhang restriction site. |
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dict
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defined(A,
dct=...)
Only the enzymes that have a defined restriction site in Rebase. |
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dict
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with_sites(A,
dct=...)
Enzymes which have at least one site in the sequence. |
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dict
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without_site(A,
dct=...)
Enzymes which have no site in the sequence. |
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dict
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with_N_sites(A,
N,
dct=...)
Enzymes which cut N times the sequence. |
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Limit the search to the enzymes named in list_of_names.
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Limit the search to the enzymes whose site is of size
<site_size>.
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dict
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only_between(A,
start,
end,
dct=...)
Enzymes that cut the sequence only in between start and end. |
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dict
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between(A,
start,
end,
dct=...)
Enzymes that cut the sequence at least in between start and end. |
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dict
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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
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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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dict
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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 sets.Set :
__as_immutable__ ,
__as_temporarily_immutable__ ,
__getstate__ ,
__hash__ ,
__iand__ ,
__ior__ ,
__isub__ ,
__ixor__ ,
__setstate__ ,
clear ,
difference_update ,
discard ,
intersection_update ,
pop ,
symmetric_difference_update ,
union_update ,
update
Inherited from sets.BaseSet :
__and__ ,
__cmp__ ,
__copy__ ,
__deepcopy__ ,
__eq__ ,
__ge__ ,
__gt__ ,
__iter__ ,
__le__ ,
__len__ ,
__lt__ ,
__ne__ ,
__or__ ,
__sub__ ,
__xor__ ,
copy ,
difference ,
intersection ,
issubset ,
issuperset ,
symmetric_difference ,
union
Inherited from sets.BaseSet (private):
_binary_sanity_check ,
_compute_hash ,
_repr ,
_update
Inherited from PrintFormat.PrintFormat :
make_format ,
print_as
Inherited from object :
__delattr__ ,
__getattribute__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__setattr__
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