Package biana :: Package BianaParser :: Module pfamParser :: Class PFAMParser
[hide private]
[frames] | no frames]

Class PFAMParser

source code


PFAM Parser Class

Instance Methods [hide private]
 
__init__(self)
Starts the bianaParser Object
source code
 
parse_database(self)
Method that implements the specific operations of PFAM parser
source code
 
parse_pfam_seq_record(self, header_line, sequence) source code
 
parse_pfam_file(self, pfamType, pfamFile) source code

Inherited from bianaParser.BianaParser: add_to_log, close, get_log_string, initialize_input_file_descriptor, parseArguments, print_help, start

Inherited from bianaParser.BianaParser (private): _indent, _splitsize

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

Class Variables [hide private]
  name = 'pfam'
  description = 'PFAM Parser. Collection of multiple sequence al...
  external_entity_definition = 'A external entity represents a p...
  external_entity_relations = ''
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 

Starts the bianaParser Object

Overrides: object.__init__
(inherited documentation)

parse_database(self)

source code 

Method that implements the specific operations of PFAM parser

Overrides: bianaParser.BianaParser.parse_database

Class Variable Details [hide private]

description

Value:
'PFAM Parser. Collection of multiple sequence alignments and hidden ma\
rkov models covering many common protein domains and families'

external_entity_definition

Value:
'A external entity represents a pfam domain'