Package csb :: Package bio :: Package sequence :: Class Sequence

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Class Sequence

      object --+    
               |    
AbstractSequence --+
                   |
                  Sequence

High-performance sequence object. The actual sequence is stored internally as a string. The indexer acts as a residue factory, which creates a new ResidueInfo instance each time.

Note: This class was created with parsing large volumes of data in mind. This comes at the expense of degraded performance of the sequence indexer.

Nested Classes
Inherited from `AbstractSequence`: `__metaclass__`

Instance Methods

__init__(self, id, header, residues, type=Unknown)
x.__init__(...) initializes x; see help(type(x)) for signature

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 AbstractSequence: __getitem__, __iter__, __len__, __repr__, __str__, dump

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

Class Variables
	__abstractmethods__ = `frozenset([])`
Inherited from `AbstractSequence`: `DELIMITER`

Properties

str sequence
The actual sequence

Inherited from AbstractSequence: alphabet, header, id, length, residues, type

Inherited from object: __class__

Method Details

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

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) - sequence string
type (EnumItem) - a SequenceTypes member (defaults to protein)

Overrides: object.__init__

(inherited documentation)

extract(self, positions)

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

Parameters:

positions - positions to extract

Returns: AbstractSequence

a new sequence

Raises:

SequencePositionError - if any position is out of range

Overrides: AbstractSequence.extract

(inherited documentation)

strip(self)

Remove all gaps and insertions from the sequence.

Returns: AbstractSequence: a new sequence instance, containing no gaps
Overrides: AbstractSequence.strip: (inherited documentation)

subregion(self, start, end)

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

Parameters:

start - start position
end - end position

Returns: AbstractSequence

a new sequence

Raises:

SequencePositionError - if start/end positions are out of range

Overrides: AbstractSequence.subregion

(inherited documentation)

Property Details

sequence

The actual sequence

Get Method:: unreachable.sequence(self)
Type:: str