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CSB v1.2.5.d7fd331
Package csb :: Package bio :: Package io :: Module fasta :: Class SequenceAlignmentReader
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Class SequenceAlignmentReader

source code

object --+
         |
        SequenceAlignmentReader

Sequence alignment parser.

Instance Methods
 
__init__(self, product_type=Protein, strict=True)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
A3MAlignment
read_a3m(self, string)
Parse an alignment in A3M format.		 source code
SequenceAlignment
read_fasta(self, string)
Parse an alignment in multi-FASTA format.		 source code

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

Properties
enum item product_type
Default sequence type of the alignment entries - a member of SequenceTypes
bool strict
True if strict mode is enabled

Inherited from object: __class__

Method Details

__init__(self, product_type=Protein, strict=True)
(Constructor)

source code 

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

Parameters:
Overrides: object.__init__
(inherited documentation)

read_a3m(self, string)

source code 

Parse an alignment in A3M format.

Parameters:
  • string (str) - alignment string
Returns: A3MAlignment

read_fasta(self, string)

source code 

Parse an alignment in multi-FASTA format.

Parameters:
  • string (str) - alignment string
Returns: SequenceAlignment

Property Details

product_type

Default sequence type of the alignment entries - a member of SequenceTypes

Get Method:
unreachable.product_type(self) - Default sequence type of the alignment entries - a member of SequenceTypes
Type:
enum item

strict

True if strict mode is enabled

Get Method:
unreachable.strict(self) - True if strict mode is enabled
Type:
bool

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