Package csb :: Package bio :: Package sequence :: Class A3MAlignment

Class A3MAlignment

       object --+    
                |    
AbstractAlignment --+
                    |
                   A3MAlignment

A specific type of multiple alignment, which provides some operations relative to a master sequence (the first entry in the alignment).

Nested Classes
Inherited from `AbstractAlignment`: `__metaclass__`

Instance Methods

__init__(self, sequences, strict=True)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

str

format(self, format=A3M, headers=True)
Format the alignment as a string.

source code

hmm_subregion(self, match_start, match_end)
Same as AbstractAlignment.subregion, but start/end positions are ranks in the ungapped master sequence.

source code

bool

insertion_at(self, column)
Return True of column contains at least one insertion. source code

Inherited from AbstractAlignment: __getitem__, __iter__, add, gap_at, subregion

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

Static Methods

A3MAlignment

parse(string, strict=True)
Create a new A3MAlignment from an A3M string.

source code

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
AbstractSequence	master The master sequence
int	matches Number of match states (residues in the ungapped master).
Inherited from `AbstractAlignment`: `columns`, `length`, `rows`, `size` Inherited from `object`: `__class__`

Method Details

init(self, sequences, strict=True)
(Constructor)

source code

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

Parameters:

sequences - alignment entries (must have equal length)
strict - if True, raise {DuplicateSequenceError} when a duplicate ID is found (default=True)

Overrides: object.__init__

(inherited documentation)

format(self, format=A3M, headers=True)

source code

Format the alignment as a string.

Parameters:

format - alignment format type, member of AlignmentFormats
headers - if False, omit headers

Returns: str

Overrides: AbstractAlignment.format

(inherited documentation)

insertion_at(self, column)

source code

Return True of column contains at least one insertion.

Parameters:

column (int) - column number, 1-based

Returns: bool

parse(string, strict=True)
Static Method

source code

Create a new A3MAlignment from an A3M string.

Parameters:

string (str) - MSA-formatted string
strict (bool) - see AbstractAlignment

Returns: A3MAlignment

Property Details

master

The master sequence

Get Method:: unreachable.master(self) - The master sequence
Type:: AbstractSequence

matches

Number of match states (residues in the ungapped master).

Get Method:: unreachable.matches(self) - Number of match states (residues in the ungapped master).
Type:: int

Class A3MAlignment

__init__(self, sequences, strict=True) (Constructor)

format(self, format=A3M, headers=True)

insertion_at(self, column)

parse(string, strict=True) Static Method

master

matches

init(self, sequences, strict=True)
(Constructor)

parse(string, strict=True)
Static Method