Last Modified
  2013-07-17 23:07:51 +0000
Requires

## Description

# bio/db/fasta/defline.rb - FASTA defline parser class

Copyright | Copyright (C) 2001, 2002 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>, Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $

## Description

Bio::FastaDefline is a parser class for definition line (defline) of the FASTA format.

## Examples

    rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
    rub.entry_id       ==> 'gi|671595'
    rub.get('emb')     ==> 'CAA85678.1'
    rub.emb            ==> 'CAA85678.1'
    rub.gi             ==> '671595'
    rub.accession      ==> 'CAA85678'
    rub.accessions     ==> [ 'CAA85678' ]
    rub.acc_version    ==> 'CAA85678.1'
    rub.locus          ==> nil
    rub.list_ids       ==> [["gi", "671595"],
                            ["emb", "CAA85678.1", nil],
                            ["Perovskia abrotanoides"]]

    ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
    ckr.entry_id      ==> "gi|2495000"
    ckr.sp            ==> "CCKR_CAVPO"
    ckr.pir           ==> "I51898"
    ckr.gb            ==> "AAB29504.1"
    ckr.gi            ==> "2495000"
    ckr.accession     ==> "AAB29504"
    ckr.accessions    ==> ["Q63931", "AAB29504"]
    ckr.acc_version   ==> "AAB29504.1"
    ckr.locus         ==> nil
    ckr.description   ==>
      "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
    ckr.descriptions  ==>
      ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
       "cholecystokinin A receptor - guinea pig",
       "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
    ckr.words         ==>
      ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
       "receptor", "type"]
    ckr.id_strings    ==>
      ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
       "544724", "AAB29504.1", "Cavia"]
    ckr.list_ids      ==>
      [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
       ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
       ["gb", "AAB29504.1", nil], ["Cavia"]]

## References

- FASTA format (WikiPedia) en.wikipedia.org/wiki/FASTA_format

- Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml