Last Modified
2013-07-14 11:53:07 +0000
Requires
  • bio/db
  • bio/reference
  • bio/compat/references

Description

bio/db/embl.rb - Common methods for EMBL style database classes

Copyright

Copyright (C) 2001-2006 Mitsuteru C. Nakao <n@bioruby.org>

License

The Ruby License

$Id: common.rb,v 1.12.2.5 2008/05/07 12:22:10 ngoto Exp $

Description

EMBL style databases class

This module defines a common framework among EMBL, UniProtKB, SWISS-PROT, TrEMBL. For more details, see the documentations in each embl/*.rb libraries.

EMBL style format:

ID - identification             (begins each entry; 1 per entry)
AC - accession number           (>=1 per entry)
SV - sequence version           (1 per entry)
DT - date                       (2 per entry)
DE - description                (>=1 per entry)
KW - keyword                    (>=1 per entry)
OS - organism species           (>=1 per entry)
OC - organism classification    (>=1 per entry)
OG - organelle                  (0 or 1 per entry)
RN - reference number           (>=1 per entry)
RC - reference comment          (>=0 per entry)
RP - reference positions        (>=1 per entry)
RX - reference cross-reference  (>=0 per entry)
RA - reference author(s)        (>=1 per entry)
RG - reference group            (>=0 per entry)
RT - reference title            (>=1 per entry)
RL - reference location         (>=1 per entry)
DR - database cross-reference   (>=0 per entry)
FH - feature table header       (0 or 2 per entry)
FT - feature table data         (>=0 per entry)
CC - comments or notes          (>=0 per entry)
XX - spacer line                (many per entry)
SQ - sequence header            (1 per entry)
bb - (blanks) sequence data     (>=1 per entry)
// - termination line           (ends each entry; 1 per entry)

Examples

# Make a new parser class for EMBL style database entry.
require 'bio/db/embl/common'
module Bio
  class NEWDB < EMBLDB
    include Bio::EMBLDB::Common
  end
end

References