Path: | lib/bio/db/embl/common.rb |
Last Update: | Sun Dec 04 02:16:41 +0000 2011 |
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 $
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)
# 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