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Package csb :: Package bio :: Package sequence :: Class AbstractSequence
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Class AbstractSequence

source code

object --+
         |
        AbstractSequence
Known Subclasses:

Base abstract class for all Sequence objects.

Provides 1-based access to the residues in the sequence via the sequence.residues property. The sequence object itself also behaves like a collection and provides 0-based access to its elements (residues).

Nested Classes
  __metaclass__
Metaclass for defining Abstract Base Classes (ABCs).
Instance Methods
 
__getitem__(self, spec) source code
 
__init__(self, id, header, residues, type=Unknown)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__iter__(self) source code
 
__len__(self) source code
 
__repr__(self)
repr(x)		 source code
 
__str__(self)
str(x)		 source code
 
dump(self, output_file)
Dump the sequence in FASTA format.		 source code
AbstractSequence
extract(self, positions)
Extract a subsequence, defined by a list of 1-based positions.		 source code
AbstractSequence
strip(self)
Remove all gaps and insertions from the sequence.		 source code
AbstractSequence
subregion(self, start, end)
Extract a subsequence, defined by [start, end].		 source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Variables
  DELIMITER = '>'
  __abstractmethods__ = frozenset(['_add', '_get'])
Properties
csb.core.enum alphabet
The sequence alphabet corresponding to the current sequence type
str header
Sequence description
str id
Sequence identifier
int length
Number of residues
SequenceIndexer residues
Rank-based access to the underlying residues
str sequence
The actual sequence
enum item type
Sequence type - a member of SequenceTypes

Inherited from object: __class__

Method Details

__init__(self, id, header, residues, type=Unknown)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • id (str) - FASTA ID of this sequence (e.g. accession number)
  • header (str) - FASTA sequence header
  • residues (str or collection of ResidueInfo) - sequence residues
  • type (EnumItem) - a SequenceTypes member (defaults to protein)
Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

repr(x)

Overrides: object.__repr__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 

str(x)

Overrides: object.__str__
(inherited documentation)

dump(self, output_file)

source code 

Dump the sequence in FASTA format.

Parameters:
  • output_file (str or stream) - write the output to this file or stream

extract(self, positions)

source code 

Extract a subsequence, defined by a list of 1-based positions.

Parameters:
  • positions (tuple of int) - positions to extract
Returns: AbstractSequence
a new sequence
Raises:

strip(self)

source code 

Remove all gaps and insertions from the sequence.

Returns: AbstractSequence
a new sequence instance, containing no gaps

subregion(self, start, end)

source code 

Extract a subsequence, defined by [start, end]. The start and end positions are 1-based, inclusive.

Parameters:
  • start (int) - start position
  • end (int) - end position
Returns: AbstractSequence
a new sequence
Raises:

Property Details

alphabet

The sequence alphabet corresponding to the current sequence type

Get Method:
unreachable.alphabet(self) - The sequence alphabet corresponding to the current sequence type
Type:
csb.core.enum

header

Sequence description

Get Method:
unreachable.header(self) - Sequence description
Set Method:
unreachable.header(self, value)
Type:
str

id

Sequence identifier

Get Method:
unreachable.id(self) - Sequence identifier
Set Method:
unreachable.id(self, value)
Type:
str

length

Number of residues

Get Method:
unreachable.length(self) - Number of residues
Type:
int

residues

Rank-based access to the underlying residues

Get Method:
unreachable.residues(self) - Rank-based access to the underlying residues
Type:
SequenceIndexer

sequence

The actual sequence

Get Method:
unreachable.sequence(self) - The actual sequence
Type:
str

type

Sequence type - a member of SequenceTypes

Get Method:
unreachable.type(self) - Sequence type - a member of SequenceTypes
Set Method:
unreachable.type(self, value)
Type:
enum item

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