Package csb :: Package bio :: Package io :: Module fasta :: Class BaseSequenceParser |
[frames] | no frames]

# Class BaseSequenceParser

source code

    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) | source code
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) | source code
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) | source code
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) | source code
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) | source code
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