|   | dbxresource | 
Please help by correcting and extending the Wiki pages.
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:6.6.0.0
   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 | 
 | * | ||||||||||||||||||||||||||||||||||||
| -[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 Secpages 0 Order 64 Fill 52 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 22 Fullcount 22 Kwlimit 18 Reffiles 0 | 
| Type Secondary Compress Yes Pages 3 Secpages 21 Order 27 Fill 25 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 21 Fullcount 74 Kwlimit 60 Idlimit 32 | 
| Type Secondary Compress Yes Pages 32 Secpages 905 Order 60 Fill 49 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 829 Fullcount 2006 Kwlimit 20 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 69 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 61 Fullcount 152 Kwlimit 15 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 32 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 11 Fullcount 135 Kwlimit 15 Idlimit 32 | 
| Type Secondary Compress Yes Pages 4 Secpages 110 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 106 Fullcount 201 Kwlimit 15 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 71 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 67 Fullcount 192 Kwlimit 15 Idlimit 32 | 
| Type Identifier Compress Yes Pages 6 Secpages 0 Order 44 Fill 38 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 110 Fullcount 110 Kwlimit 32 Reffiles 0 | 
| Type Secondary Compress Yes Pages 12 Secpages 361 Order 60 Fill 49 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 335 Fullcount 659 Kwlimit 20 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 37 Order 46 Fill 39 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 16 Fullcount 148 Kwlimit 30 Idlimit 32 | 
| Type Secondary Compress Yes Pages 12 Secpages 130 Order 25 Fill 23 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 126 Fullcount 206 Kwlimit 65 Idlimit 32 | 
| Type Secondary Compress Yes Pages 11 Secpages 124 Order 19 Fill 18 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 120 Fullcount 169 Kwlimit 90 Idlimit 32 | 
| Type Secondary Compress Yes Pages 33 Secpages 900 Order 46 Fill 39 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 729 Fullcount 2147 Kwlimit 30 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 12 Order 60 Fill 49 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 12 Fullcount 43 Kwlimit 20 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 17 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 5 Fullcount 83 Kwlimit 15 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 18 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 18 Fullcount 23 Kwlimit 15 Idlimit 32 | 
| Type Secondary Compress Yes Pages 3 Secpages 40 Order 104 Fill 75 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 26 Fullcount 114 Kwlimit 6 Idlimit 32 | 
| Type Secondary Compress Yes Pages 11 Secpages 268 Order 52 Fill 44 Level 0 Pagesize 2048 Cachesize 20000 Order2 10 Fill2 13 Secpagesize 512 Seccachesize 20000 Count 227 Fullcount 585 Kwlimit 25 Idlimit 32 | 
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
| 
Processing directory: /homes/user/test/data/
Processing file: DRCAT.dat
entries: 110 (110) time: 0.0s (0.0s)
Total time: 0.0s
Entry idlen 32 OK. Maximum ID length was 28 for 'WORLD_2DPAGE_CGL14067_2DPAGE'.
Field acc acclen 18 OK. Maximum acc term length was 18 for 'REPRODUCTION2DPAGE'.
Field nam namlen 20 OK. Maximum nam term length was 16 for 'characterization'.
Field des deslen 20 OK. Maximum des term length was 17 for 'transcriptionally'.
Field url urllen 25 OK. Maximum url term length was 17 for 'compluyeast2dpage'.
Field cat catlen 60 OK. Maximum cat term length was 40 for 'Protein sequence classification database'.
Field taxid taxidlen 6 OK. Maximum taxid term length was 5 for '40674'.
Field edat edatlen 15 OK. Maximum edat term length was 4 for '2378'.
Field etpc etpclen 15 OK. Maximum etpc term length was 4 for '0166'.
Field eid eidlen 15 OK. Maximum eid term length was 4 for '1116'.
Field efmt efmtlen 15 OK. Maximum efmt term length was 4 for '2331'.
Field qout qoutlen 90 OK. Maximum qout term length was 85 for 'Protein report (transcription factor) {Documented regulators of a given set of genes}'.
Field qfmt qfmtlen 30 OK. Maximum qfmt term length was 14 for 'HTML {graphic}'.
Field qin qinlen 65 OK. Maximum qin term length was 43 for 'Sequence accession (protein) {World-2DPAGE}'.
Field qurl qurllen 30 OK. Maximum qurl term length was 29 for 'identificationAccessionNumber'.
Field xref xreflen 15 OK. Maximum xref term length was 13 for 'EMBL_explicit'.
Field rest restlen 20 OK. Maximum rest term length was 19 for 'prideMartWebService'.
Field soap soaplen 15 OK. Maximum soap term length was 12 for 'dataservices'.
 | 
| 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.