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
• INSD XML

fasta

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

embl

• 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

genbank

• 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

swiss-prot

• 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