= !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