| | 1 | = !BioJava = |
| | 2 | Working with BioJava-live SVN version 4723. |
| | 3 | == Fasta Format == |
| | 4 | === Major Issues === |
| | 5 | None |
| | 6 | === Minor Issues === |
| | 7 | Sequence case is not preserved. Line length varies (default is 80 cpl). |
| | 8 | ===Read-Write-Read=== |
| | 9 | Succeeds! |
| | 10 | |
| | 11 | |
| | 12 | == Genbank format == |
| | 13 | === Major Issues === |
| | 14 | None. |
| | 15 | === Minor Issues === |
| | 16 | Feature qualifier order is not preserved. |
| | 17 | Because NCBI Taxonomy is referenced from memory or database if the version used |
| | 18 | doesn't match the version that was used to construct the record then minor |
| | 19 | differences appear. For example the common name of Arabidopsis changed from thale cress |
| | 20 | to mouse ear cress. |
| | 21 | ===Read-Write-Read=== |
| | 22 | Success! |
| | 23 | |
| | 24 | == GenbankXML format == |
| | 25 | == Major Issues == |
| | 26 | Not supported (INSD is). |
| | 27 | |
| | 28 | == INSD Format == |
| | 29 | == Major Issues == |
| | 30 | None. |
| | 31 | == Minor Issues == |
| | 32 | * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 |
| | 33 | {{{ |
| | 34 | <INSDReference_position>1..1</INSDReference_position> |
| | 35 | }}} |
| | 36 | * There are other examples of this redundancy. I think if this doesn't break the |
| | 37 | dtd then it doesn't matter. |
| | 38 | * Qualifiers order is not preserved. I don't think this matters. |
| | 39 | ===Read-Write-Read=== |
| | 40 | Success! |
| | 41 | |
| | 42 | == EMBL Format == |
| | 43 | === Major Issues === |
| | 44 | No major issues |
| | 45 | === Minor Issues === |
| | 46 | * Version in date is not correct on output. |
| | 47 | * Two XX lines after references. |
| | 48 | * Feature qualifiers out of order. |
| | 49 | ===Read-Write-Read=== |
| | 50 | Succeeds! |
| | 51 | |
| | 52 | == SwissProt/ Uniprot == |
| | 53 | === Major Issues === |
| | 54 | === Minor Issues === |
| | 55 | * BioSQL cannot store more than one database reference for a single publication, |
| | 56 | eg Pubmed and medline Id and DOI. |
| | 57 | * We are putting 'and' before the last author. |
| | 58 | * We loose the copyright statement. |
| | 59 | ===Read-Write-Read=== |
| | 60 | Cannot read back in: |
| | 61 | |
| | 62 | <code> |
| | 63 | Format_object=org.biojavax.bio.seq.io.UniProtFormat |
| | 64 | Accession=Q43385 |
| | 65 | Id= |
| | 66 | Comments= |
| | 67 | Parse_block=OS Arabidopsis thaliana (Mouse-ear cress) (Arabidopsis thaliana (L.) Heynh.).OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;OS Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; |
| | 68 | eurosids II; Brassicales; Brassicaceae; Arabidopsis.OX NCBI_TaxID=3702; |
| | 69 | Stack trace follows .... |
| | 70 | |
| | 71 | |
| | 72 | at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:615) |
| | 73 | at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) |
| | 74 | ... 3 more |
| | 75 | Caused by: java.lang.IllegalArgumentException: NCBI taxonomy names cannot embed new lines - at:74, in name: <Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; |
| | 76 | eurosids II; Brassicales; Brassicaceae; Arabidopsis> |
| | 77 | at org.biojavax.bio.taxa.SimpleNCBITaxonName.<init>(SimpleNCBITaxonName.java:47) |
| | 78 | at org.biojavax.bio.taxa.SimpleNCBITaxon.addName(SimpleNCBITaxon.java:148) |
| | 79 | at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:339) |
| | 80 | ... 4 more |
| | 81 | </code> |
| | 82 | |
| | 83 | == UniprotXML == |
| | 84 | === Major Issues === |
| | 85 | * Missing the namespace and the version from entry tag |
| | 86 | * Don't write editor list if there are no editors |
| | 87 | * Reference tag not correctly constructed. |
| | 88 | * When writing Uniprot XML it would be illegal to use anything other than |
| | 89 | Swiss-Prot or TrEMBL as the Namespace |
| | 90 | === Minor Issues === |
| | 91 | ===Read-Write-Read=== |
| | 92 | |
| | 93 | == EMBLxml == |
| | 94 | === Major Issues === |
| | 95 | none |
| | 96 | === Minor Issues === |
| | 97 | ===Read-Write-Read=== |
| | 98 | Success! |
