BioPerl Outstanding Issues in roundtripping

At bioperl-live SVN revision 14544.

All known issues below are classified as minor.

fasta

* possible minor issue: BioPerl does not parse in sequence version nor fasta from genbank with a gi number. BioRuby does that. Should we?

genbank

* FT qualifier lines are not returned in order

embl

• minor: only the actual date on the DT (date) line is kept, release information and document version is lost.
  • Note: We now track only the sequence version from the ID line, not the document version from the second DT line.
  • Note: BioSQL can store both versions. Should we update the BioPerl Bio::Seq::RichSeqI API to have document version, too?

    DT   27-FEB-1998 (Rel. 54, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 6)
    ->
    DT   27-FEB-1998
    DT   14-NOV-2006
    

• minor: Word wrapping differences if free text lines, especially in author lists ** Line 'RL Submitted (date) to the EMBL/GenBank/DDBJ databases.' is shorter then 80, so the affiliation from the following line gets wrapped into this line.
• minor: the feature key/value pairs (FT) are not returned in order

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