[BioRuby-cvs] bioruby/lib/bio/db/genbank genbank.rb, 0.40.2.3, 0.40.2.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv21173/lib/bio/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	genbank.rb 
Log Message:
* Bio::GenBank#to_biosequence is changed to imporve support of sequence output
  and data exchange.
* Bio::GenBank#date_created is added. It returns Date object.


Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.40.2.3
retrieving revision 0.40.2.4
diff -C2 -d -r0.40.2.3 -r0.40.2.4
*** genbank.rb	4 Mar 2008 09:22:35 -0000	0.40.2.3
--- genbank.rb	17 Jun 2008 15:56:18 -0000	0.40.2.4
***************
*** 8,13 ****
--- 8,16 ----
  #
  
+ require 'date'
  require 'bio/db'
  require 'bio/db/genbank/common'
+ require 'bio/sequence'
+ require 'bio/sequence/dblink'
  
  module Bio
***************
*** 122,129 ****
--- 125,142 ----
    alias nalen length
  
+   # (obsolete???) length of the sequence
    def seq_len
      seq.length
    end
  
+   # modified date. Returns Date object, String or nil.
+   def date_modified
+     begin
+       Date.parse(self.date)
+     rescue ArgumentError, TypeError, NoMethodError, NameError
+       self.date
+     end
+   end
+ 
    # converts Bio::GenBank to Bio::Sequence
    # ---
***************
*** 132,135 ****
--- 145,156 ----
    def to_biosequence
      sequence = Bio::Sequence.new(seq)
+ 
+     sequence.id_namespace = 
+       if /\_/ =~ self.accession.to_s then
+         'RefSeq'
+       else
+         'GenBank'
+       end
+ 
      sequence.entry_id = self.entry_id
  
***************
*** 137,147 ****
      sequence.secondary_accessions = self.accessions - [ self.accession ]
  
      sequence.molecule_type = self.natype
      sequence.division = self.division
      sequence.topology = self.circular
  
      sequence.sequence_version = self.version
      #sequence.date_created = nil #????
!     sequence.date_modified = self.date
  
      sequence.definition = self.definition
--- 158,177 ----
      sequence.secondary_accessions = self.accessions - [ self.accession ]
  
+     if /GI\:(.+)/ =~ self.gi.to_s then
+       sequence.other_seqids = [ Bio::Sequence::DBLink.new('GI', $1) ]
+     end
+ 
      sequence.molecule_type = self.natype
      sequence.division = self.division
      sequence.topology = self.circular
+     sequence.strandedness = case self.strand.to_s.downcase;
+                             when 'ss-'; 'single';
+                             when 'ds-'; 'double';
+                             when 'ms-'; 'mixed';
+                             else nil; end
  
      sequence.sequence_version = self.version
      #sequence.date_created = nil #????
!     sequence.date_modified = date_modified
  
      sequence.definition = self.definition
***************
*** 149,153 ****
      sequence.species = self.organism
      sequence.classification = self.taxonomy.to_s.sub(/\.\z/, '').split(/\s*\;\s*/)
!     #sequence.organnella = nil # not used
      sequence.comments = self.comment
      sequence.references = self.references
--- 179,183 ----
      sequence.species = self.organism
      sequence.classification = self.taxonomy.to_s.sub(/\.\z/, '').split(/\s*\;\s*/)
!     #sequence.organelle = nil # yet unsupported
      sequence.comments = self.comment
      sequence.references = self.references