Package csb :: Package bio :: Package io :: Module fasta :: Class BaseSequenceParser

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Class BaseSequenceParser

object --+
         |
        BaseSequenceParser

Known Subclasses:

SequenceParser

FASTA parser template. Subclasses must implement the way FASTA strings are handled by overriding BaseSequenceParser.read_sequence.

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

__init__(self, product=<class 'csb.bio.sequence.Sequence'>, product_type=Protein)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

SequenceCollection

parse_file(self, fasta_file)
Read FASTA sequences from a (m)FASTA file

source code

SequenceCollection

parse_string(self, fasta_string)
Read FASTA sequences from an (m)FASTA-formatted string

source code

iterator

read(self, fasta_file)
Read FASTA sequences from an (m)FASTA file.

source code

AbstractSequence

read_sequence(self, string)
Parse a single FASTA string

source code

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

Class Variables
	__abstractmethods__ = `frozenset(['read_sequence'])`

Properties
class	product_factory Factory used to build sequence products
enum item	product_type Default sequence type of the products - a member of SequenceTypes
Inherited from `object`: `__class__`

Method Details

init(self, product=<class 'csb.bio.sequence.Sequence'>, product_type=Protein)
(Constructor)

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

Parameters:

product (type) - sequence product factory (an AbstractSequence subclass)
product_type (EnumItem) - default SequenceTypes member for the products

Overrides: object.__init__

(inherited documentation)

parse_file(self, fasta_file)

Read FASTA sequences from a (m)FASTA file

Parameters:

fasta_file (str, file) - input FASTA file name or opened stream

Returns: SequenceCollection

a list of Sequences

Raises:

SequenceFormatError - on parse error

parse_string(self, fasta_string)

Read FASTA sequences from an (m)FASTA-formatted string

Parameters:

fasta_string (str) - FASTA string to parse

Returns: SequenceCollection

a list of Sequences

Raises:

SequenceFormatError - on parse error

read(self, fasta_file)

Read FASTA sequences from an (m)FASTA file.

Parameters:

fasta_file (str, file) - input FASTA file name or opened stream

Returns: iterator

efficient cursor over all Sequences (parse on demand)

Raises:

SequenceFormatError - on parse error

read_sequence(self, string)

Parse a single FASTA string

Returns: AbstractSequence

a new sequence, created with BaseSequenceParser.product_factory

Raises:

SequenceFormatError - on parse error

Property Details

product_factory

Factory used to build sequence products

Get Method:: unreachable.product_factory(self) - Factory used to build sequence products
Type:: class

product_type

Default sequence type of the products - a member of SequenceTypes

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