| | 1 | = !BioPerl Round Trip , First Pass = |
| | 2 | |
| | 3 | Initial evaluation of sequence format roundtrips: flat file -> !BioPerl object -> same flat file format |
| | 4 | |
| | 5 | Based on SVN revision 14501. |
| | 6 | |
| | 7 | !BioPerl does not have parsers for these formats: |
| | 8 | |
| | 9 | * asn1 |
| | 10 | * genbank XML |
| | 11 | * insd XML |
| | 12 | |
| | 13 | == fasta == |
| | 14 | |
| | 15 | * minor: the length of the sequence line can vary (settable within Bio::SeqIO::fasta object) |
| | 16 | |
| | 17 | == embl == |
| | 18 | |
| | 19 | * MAJOR: sequence name and accession lost in conversion |
| | 20 | * MAJOR: OX line for !TaxId is lost |
| | 21 | * minor: the feature key/value pairs (FT) are not returned in order |
| | 22 | * minor: SQ line does not contain CRC32 value |
| | 23 | |
| | 24 | |
| | 25 | == genbank == |
| | 26 | |
| | 27 | * MAJOR: SOURCE line adds full stop to the end of the line (following old genbank conversion?) |
| | 28 | * minor: line BASE not present in recent genbank file, still generated by bioperl |
| | 29 | * minor: features are not returned in order |
| | 30 | |
| | 31 | == swiss-prot == |
| | 32 | |
| | 33 | * minor: No full stop at the end of the DT lines |
| | 34 | * MAJOR: GN line not returning only value from key/value paris (e.g. |
| | 35 | {{{ |
| | 36 | GN Name=DOF3.7; Synonyms=BBFA, DAG1;... |
| | 37 | -> |
| | 38 | GN DOF3.7 OR BBFA OR DAG1 ... |
| | 39 | }}} |
| | 40 | * minor: OC line word wrapping differences |
| | 41 | * minor: extra spaces at the end of the first RT line when there are more than one of them |
| | 42 | * MAJOR: RX line:DOI key/value pair lost |
| | 43 | * MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines |
| | 44 | * minor: extra space after first FT line |
| | 45 | * minor: FTid sometimes not written on its own line |
| | 46 | * minor: extra space written to the end of the sequence line |
| | 47 | |
