BioPerl Round Trip , First Pass

Initial evaluation of sequence format roundtrips: flat file -> BioPerl object -> same flat file format

Based on bioperl-live SVN revision 14501.

BioPerl does not have parsers for these formats:

  • ASN.1
  • genbank XML


  • minor: the length of the sequence line can vary (settable using method Bio::SeqIO::fasta::width() )


  • MAJOR: sequence name and accession lost in conversion
  • MAJOR: OX line for TaxId is lost
  • minor: the feature key/value pairs (FT) are not returned in order
  • minor: SQ line does not contain CRC32 value


  • MAJOR: SOURCE line adds full stop to the end of the line (following old genbank conversion?)
  • minor: line BASE not present in recent genbank file, still generated by bioperl
  • minor: features are not returned in order


  • minor: No full stop at the end of the DT lines
  • MAJOR: GN line returning only value from key/value pairs (e.g.
    GN   Name=DOF3.7; Synonyms=BBFA, DAG1;...   
    GN   DOF3.7 OR BBFA OR DAG1 ...
  • minor: OC line word wrapping differences
  • minor: extra spaces at the end of the first RT line when there are more than one of them
  • MAJOR: RX line:DOI key/value pair lost
  • MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines
  • minor: extra space after first FT line
  • minor: FTid sometimes not written on its own line
  • minor: extra space written to the end of the sequence line