dbxresource |
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These indexes allow access of flat files larger than 2Gb.
% dbxresource drcat Index a data resource catalogue using b+tree indices Standard database name [drcat]: drcat Resource name [drcatresource]: drcatresource Database directory [.]: Wildcard database filename [DRCAT.dat]: DRCAT.dat id : ID acc : IDother nam : Name des : Description url : Server URL cat : Category name taxid : Taxon id edat : EDAM data term efmt : EDAM format term eid : EDAM data id term etpc : EDAM topic term xref : Link qout : Query output qfmt : Query output format qin : Query input parameters qurl : Query URL rest : Rest URL soap : SOAP URL Index fields [*]: Compressed index files [Y]: General log output file [outfile.dbxresource]: |
Go to the output files for this example
Index a data resource catalogue using b+tree indices Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string [drcat] Basename for index files (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-standardname] string [$(dbname)] Standard database name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-dbresource] string [drcatresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -filenames string [DRCAT.dat] Wildcard database filename (Any string) -fields menu [*] Index fields (Values: id (ID); acc (IDother); nam (Name); des (Description); url (Server URL); cat (Category name); taxid (Taxon id); edat (EDAM data term); efmt (EDAM format term); eid (EDAM data id term); etpc (EDAM topic term); xref (Link); qout (Query output); qfmt (Query output format); qin (Query input parameters); qurl (Query URL); rest (Rest URL); soap (SOAP URL)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxresource] General log output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -release string [0.0] Release number (Any string up to 9 characters) -date string [00/00/00] Index date (Date string dd/mm/yy) -exclude string Wildcard filename(s) to exclude (Any string) -indexoutdir outdir [.] Index file output directory Associated qualifiers: "-directory" associated qualifiers -extension string Default file extension "-indexoutdir" associated qualifiers -extension string Default file extension "-outfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||
[-dbname] (Parameter 1) |
string | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | drcat | ||||||||||||||||||||||||||||||||||||
[-standardname] (Parameter 2) |
string | Standard database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | $(dbname) | ||||||||||||||||||||||||||||||||||||
[-dbresource] (Parameter 3) |
string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | drcatresource | ||||||||||||||||||||||||||||||||||||
-directory | directory | Database directory | Directory | . | ||||||||||||||||||||||||||||||||||||
-filenames | string | Wildcard database filename | Any string | DRCAT.dat | ||||||||||||||||||||||||||||||||||||
-fields | list | Index fields |
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* | ||||||||||||||||||||||||||||||||||||
-[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
-outfile | outfile | General log output file | Output file | <*>.dbxresource | ||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||
-release | string | Release number | Any string up to 9 characters | 0.0 | ||||||||||||||||||||||||||||||||||||
-date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||||||||||||||||||||||||||
-exclude | string | Wildcard filename(s) to exclude | Any string | |||||||||||||||||||||||||||||||||||||
-indexoutdir | outdir | Index file output directory | Output directory | . | ||||||||||||||||||||||||||||||||||||
Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||
"-directory" associated directory qualifiers | ||||||||||||||||||||||||||||||||||||||||
-extension | string | Default file extension | Any string | |||||||||||||||||||||||||||||||||||||
"-indexoutdir" associated outdir qualifiers | ||||||||||||||||||||||||||||||||||||||||
-extension | string | Default file extension | Any string | |||||||||||||||||||||||||||||||||||||
"-outfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
General qualifiers | ||||||||||||||||||||||||||||||||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database DRCAT.dat |
Type Identifier Compress Yes Pages 3 Order 64 Fill 43 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 21 Fullcount 21 Kwlimit 18 |
Type Secondary Compress Yes Pages 60 Order 37 Fill 29 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 19 Fullcount 72 Kwlimit 40 |
Type Secondary Compress Yes Pages 2539 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 835 Fullcount 2001 Kwlimit 20 |
Type Secondary Compress Yes Pages 198 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 65 Fullcount 150 Kwlimit 15 |
Type Secondary Compress Yes Pages 37 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 11 Fullcount 135 Kwlimit 15 |
Type Secondary Compress Yes Pages 328 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 108 Fullcount 197 Kwlimit 15 |
Type Secondary Compress Yes Pages 204 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 67 Fullcount 204 Kwlimit 15 |
Type Identifier Compress Yes Pages 8 Order 44 Fill 33 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 110 Fullcount 110 Kwlimit 32 |
Type Secondary Compress Yes Pages 1021 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 335 Fullcount 659 Kwlimit 20 |
Type Secondary Compress Yes Pages 52 Order 46 Fill 34 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 16 Fullcount 148 Kwlimit 30 |
Type Secondary Compress Yes Pages 377 Order 25 Fill 21 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 122 Fullcount 204 Kwlimit 65 |
Type Secondary Compress Yes Pages 391 Order 19 Fill 17 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 126 Fullcount 169 Kwlimit 90 |
Type Secondary Compress Yes Pages 2252 Order 46 Fill 34 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 737 Fullcount 2118 Kwlimit 30 |
Type Secondary Compress Yes Pages 39 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 12 Fullcount 43 Kwlimit 20 |
Type Secondary Compress Yes Pages 15 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 4 Fullcount 87 Kwlimit 15 |
Type Secondary Compress Yes Pages 57 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 18 Fullcount 23 Kwlimit 15 |
Type Secondary Compress Yes Pages 82 Order 104 Fill 58 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 26 Fullcount 114 Kwlimit 6 |
Type Secondary Compress Yes Pages 709 Order 52 Fill 37 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 231 Fullcount 594 Kwlimit 25 |
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Processing directory: /homes/user/test/data/ Processing file: DRCAT.dat entries: 110 (110) time: 0.0s (0.0s) Total time: 0.0s |
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Index a fasta file database |
dbiflat | Index a flat file database |
dbigcg | Index a GCG formatted database |
dbxcompress | Compress an uncompressed dbx index |
dbxedam | Index the EDAM ontology using b+tree indices |
dbxfasta | Index a fasta file database using b+tree indices |
dbxflat | Index a flat file database using b+tree indices |
dbxgcg | Index a GCG formatted database using b+tree indices |
dbxobo | Index an obo ontology using b+tree indices |
dbxreport | Validate index and report internals for dbx databases |
dbxstat | Dump statistics for dbx databases |
dbxtax | Index NCBI taxonomy using b+tree indices |
dbxuncompress | Uncompress a compressed dbx index |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.