Package tfasta :: Module tfasta_templates :: Class _t

Class _t

This class is essentially a namespace to hold some values that will be used to provide templates for the TEMPLATES dict.

Instance Methods

[hide private]

__init__(self)
Will raise a RuntimeError if called. source code

Class Variables

[hide private]

_default_regex = re.compile(r'^> *(.*)$')

_default_fields = ('name')

_default_template = TEMPLATES ['default']

_swissprot_regex = re.compile(r'^>gi\|([^\|]*)\|sp\|([^\|]*)\|...

_swissprot_fields = ('gi_num', 'accession', 'description')

_swissprot_template = TEMPLATES ['swissprot']

_pdb_regex = re.compile(r'^>(....)_(\S*)\s+[^:]*:(\S*)\s+lengt...

_pdb_fields = ('idCode', 'chainID', 'type', 'numRes', 'descrip...

_pdb_template = TEMPLATES ['pdb']

_nr_regex = re.compile(r'^>gi\|([^\|]*)\|[^\|]*\|([^\|]*)\|\s*...

_nr_fields = ('gi', 'accession', 'description', 'source')

_nr_template = TEMPLATES ['nr']

_nrblast_regex = re.compile(r'^>gi\|([^\|]*)\|[^\|]*\|([^\|]*)...

_nrblast_fields = ('gi', 'accession')

_nrblast_template = TEMPLATES ['nrblast']

Method Details

[hide private]

init(self)
(Constructor)

source code

Will raise a RuntimeError if called.

Raises:

RuntimeError - raises a RuntimeError under all circumstances

Class Variable Details

[hide private]

_swissprot_regex

Value:

re.compile(r'^>gi\|([^\|]*)\|sp\|([^\|]*)\|(.*)$')

_pdb_regex

Value:

re.compile(r'^>(....)_(\S*)\s+[^:]*:(\S*)\s+length:(\S*)\s+(\S*.*)$')

_pdb_fields

Value:

('idCode', 'chainID', 'type', 'numRes', 'description')

_nr_regex

Value:

re.compile(r'^>gi\|([^\|]*)\|[^\|]*\|([^\|]*)\|\s*([^\[]*)\s*\[([^\]]*
)\]\s*$')

_nrblast_regex

Value:

re.compile(r'^>gi\|([^\|]*)\|[^\|]*\|([^\|]*)\|.*$')

Class _t

__init__(self) (Constructor)

_swissprot_regex

_pdb_regex

_pdb_fields

_nr_regex

_nrblast_regex

init(self)
(Constructor)