Changes between Version 2 and Version 3 of BioJavaRoundTripThirdPass
- Timestamp:
- 2008/02/14 12:50:33 (16 years ago)
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BioJavaRoundTripThirdPass
v2 v3 1 1 = !BioJava = 2 Working with BioJava-live SVN version 4723.2 * Working with BioJava-live SVN version 4723. 3 3 == Fasta Format == 4 4 === Major Issues === 5 None5 * None 6 6 === Minor Issues === 7 Sequence case is not preserved. --not really a bug. It is preserved if you pass in a masked alphabet instead of the default DNA alphabet.8 Line length varies (default is 80 cpl).7 * Sequence case is not preserved. --not really a bug. It is preserved if you pass in a masked alphabet instead of the default DNA alphabet. 8 * Line length varies (default is 80 cpl). 9 9 ===Read-Write-Read=== 10 Succeeds!10 * Succeeds! 11 11 12 12 13 13 == Genbank format == 14 14 === Major Issues === 15 None.15 * None. 16 16 === Minor Issues === 17 Feature qualifier order is not preserved.18 Because NCBI Taxonomy is referenced from memory or database if the version used17 * Feature qualifier order is not preserved. --it is, but xrefs and organism are moved to end of list as they are not stored internally as qualifiers. 18 * Because NCBI Taxonomy is referenced from memory or database if the version used 19 19 doesn't match the version that was used to construct the record then minor 20 20 differences appear. For example the common name of Arabidopsis changed from thale cress 21 21 to mouse ear cress. 22 22 ===Read-Write-Read=== 23 Success!23 * Success! 24 24 25 25 == GenbankXML format == 26 26 == Major Issues == 27 Not supported (INSD is).27 * Not supported (INSD is). 28 28 29 29 == INSD Format == 30 30 == Major Issues == 31 None.31 * None. 32 32 == Minor Issues == 33 * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..133 * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 34 34 {{{ 35 35 <INSDReference_position>1..1</INSDReference_position> 36 36 }}} 37 * There are other examples of this redundancy. I think if this doesn't break the37 * There are other examples of this redundancy. I think if this doesn't break the 38 38 dtd then it doesn't matter. 39 * Qualifiers order is not preserved. I don't think this matters. 39 * Qualifiers order is not preserved. I don't think this matters. --see Genbank 40 40 ===Read-Write-Read=== 41 Success!41 * Success! 42 42 43 43 == EMBL Format == 44 44 === Major Issues === 45 No major issues45 * No major issues 46 46 === Minor Issues === 47 47 * Version in date is not correct on output. --fixed 48 48 * Two XX lines after references. -- fixed 49 * Feature qualifiers out of order. 49 * Feature qualifiers out of order. --see Genbank 50 50 ===Read-Write-Read=== 51 Succeeds!51 * Succeeds! 52 52 53 53 == SwissProt/ Uniprot == … … 59 59 * We loose the copyright statement. -- fixed 60 60 ===Read-Write-Read=== 61 Cannot read back in: -- fixed61 * Cannot read back in: -- fixed 62 62 63 63 <code> … … 94 94 == EMBLxml == 95 95 === Major Issues === 96 none96 * none 97 97 === Minor Issues === 98 98 ===Read-Write-Read=== 99 Success!99 * Success!
