Package tfasta :: Module tfasta_templates :: Class _t
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Class _t

source code

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\|([^\|]*)\|[^\|]*\|([^\|]*)\|.*$')