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CoreBio

Package corebio :: Module seq :: Class SeqList
[frames | no frames]

Type SeqList

object --+    
         |    
      list --+
             |
            SeqList


A list of sequences. 

Status:
    Beta
Method Summary
  __init__(self, alist, alphabet, name, description)
  ords(self, alphabet)
Convert sequence list into a 2D array of ordinals.
  tally(self, alphabet)
Counts the occurrences of characters in each column.
    Inherited from list
  __add__(x, y)
x.__add__(y) <==> x+y...
  __contains__(x, y)
x.__contains__(y) <==> y in x...
  __delitem__(x, y)
x.__delitem__(y) <==> del x[y]...
  __delslice__(x, i, j)
Use of negative indices is not supported.
  __eq__(x, y)
x.__eq__(y) <==> x==y...
  __ge__(x, y)
x.__ge__(y) <==> x>=y...
  __getattribute__(...)
x.__getattribute__('name') <==> x.name...
  __getitem__(x, y)
x.__getitem__(y) <==> x[y]...
  __getslice__(x, i, j)
Use of negative indices is not supported.
  __gt__(x, y)
x.__gt__(y) <==> x>y...
  __hash__(x)
x.__hash__() <==> hash(x)...
  __iadd__(x, y)
x.__iadd__(y) <==> x+=y...
  __imul__(x, y)
x.__imul__(y) <==> x*=y...
  __iter__(x)
x.__iter__() <==> iter(x)...
  __le__(x, y)
x.__le__(y) <==> x<=y...
  __len__(x)
x.__len__() <==> len(x)...
  __lt__(x, y)
x.__lt__(y) <==> x<y...
  __mul__(x, n)
x.__mul__(n) <==> x*n...
  __ne__(x, y)
x.__ne__(y) <==> x!=y...
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T...
  __repr__(x)
x.__repr__() <==> repr(x)...
  __reversed__(...)
L.__reversed__() -- return a reverse iterator over the list...
  __rmul__(x, n)
x.__rmul__(n) <==> n*x...
  __setitem__(x, i, y)
x.__setitem__(i, y) <==> x[i]=y...
  __setslice__(x, i, j, y)
Use of negative indices is not supported.
  append(...)
L.append(object) -- append object to end...
  count(L, value)
L.count(value) -> integer -- return number of occurrences of value...
  extend(...)
L.extend(iterable) -- extend list by appending elements from the iterable...
  index(...)
L.index(value, [start, [stop]]) -> integer -- return first index of value...
  insert(...)
L.insert(index, object) -- insert object before index...
  pop(L, index)
L.pop([index]) -> item -- remove and return item at index (default last)...
  remove(...)
L.remove(value) -- remove first occurrence of value...
  reverse(...)
L.reverse() -- reverse *IN PLACE*...
  sort(...)
L.sort(cmp=None, key=None, reverse=False) -- stable sort *IN PLACE*;...
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name...
  __reduce__(...)
helper for pickle...
  __reduce_ex__(...)
helper for pickle...
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value...
  __str__(x)
x.__str__() <==> str(x)...

Class Variable Summary
list __slots__ = ['alphabet', 'name', 'description']
member_descriptor alphabet = <member 'alphabet' of 'SeqList' objects>
member_descriptor description = <member 'description' of 'SeqList' objects...
member_descriptor name = <member 'name' of 'SeqList' objects>

Method Details

ords(self, alphabet=None) 

Convert sequence list into a 2D array of ordinals.

tally(self, alphabet=None) 

Counts the occurrences of characters in each column.

Class Variable Details

__slots__

Type:
list
Value:
['alphabet', 'name', 'description']

alphabet

Type:
member_descriptor
Value:
<member 'alphabet' of 'SeqList' objects>

description

Type:
member_descriptor
Value:
<member 'description' of 'SeqList' objects>

name

Type:
member_descriptor
Value:
<member 'name' of 'SeqList' objects>

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