Package csb :: Package bio :: Package sequence :: Class A3MAlignment |
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# Class A3MAlignment

source code

           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