EMBOSS: dbxresource

| dbxresource

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Index a data resource catalogue using b+tree indices

## Description

dbxresource indexes the Data Resource Catalogue, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

These indexes allow access of flat files larger than 2Gb.

## Usage

Here is a sample session with dbxresource

    % 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

## Command line arguments

    Index a data resource catalogue using b+tree indices
    Version: EMBOSS:6.5.6.0

       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 |
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 | 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

## Input file format

dbxresource reads and indexes the Data Resource Catalogue DRCAT.dat file.

## Output file format

dbxresource creates one summary file for the database and two files for each field indexed.

- dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
- dbalias.xid is the B+tree index file for the ID names. It is a binary file.
- dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

  ### Output files for usage example

  ### File: drcat.ent

      # Number of files: 1
      # Release: 0.0
      # Date:    00/00/00
      Single filename database
      DRCAT.dat

  ### File: drcat.pxac

      Type         Identifier
      Compress     Yes
      Pages        3
      Secpages     0
      Order        64
      Fill         52
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        41
      Secpagesize  512
      Seccachesize 2000
      Count        22
      Fullcount    22
      Kwlimit      18
      Reffiles     0

  ### File: drcat.pxcat

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     21
      Order        27
      Fill         25
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        21
      Fullcount    74
      Kwlimit      60
      Idlimit      32

  ### File: drcat.pxde

      Type         Secondary
      Compress     Yes
      Pages        32
      Secpages     905
      Order        60
      Fill         49
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        829
      Fullcount    2006
      Kwlimit      20
      Idlimit      32

  ### File: drcat.pxedat

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     69
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        61
      Fullcount    152
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxefmt

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     32
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        11
      Fullcount    135
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxeid

      Type         Secondary
      Compress     Yes
      Pages        4
      Secpages     110
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        106
      Fullcount    201
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxetpc

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     71
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        67
      Fullcount    192
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxid

      Type         Identifier
      Compress     Yes
      Pages        6
      Secpages     0
      Order        44
      Fill         38
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       22
      Fill2        41
      Secpagesize  512
      Seccachesize 2000
      Count        110
      Fullcount    110
      Kwlimit      32
      Reffiles     0

  ### File: drcat.pxnm

      Type         Secondary
      Compress     Yes
      Pages        12
      Secpages     361
      Order        60
      Fill         49
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        335
      Fullcount    659
      Kwlimit      20
      Idlimit      32

  ### File: drcat.pxqfmt

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     37
      Order        46
      Fill         39
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        16
      Fullcount    148
      Kwlimit      30
      Idlimit      32

  ### File: drcat.pxqin

      Type         Secondary
      Compress     Yes
      Pages        12
      Secpages     130
      Order        25
      Fill         23
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        126
      Fullcount    206
      Kwlimit      65
      Idlimit      32

  ### File: drcat.pxqout

      Type         Secondary
      Compress     Yes
      Pages        11
      Secpages     124
      Order        19
      Fill         18
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        120
      Fullcount    169
      Kwlimit      90
      Idlimit      32

  ### File: drcat.pxqurl

      Type         Secondary
      Compress     Yes
      Pages        33
      Secpages     900
      Order        46
      Fill         39
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        729
      Fullcount    2147
      Kwlimit      30
      Idlimit      32

  ### File: drcat.pxrest

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     12
      Order        60
      Fill         49
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        12
      Fullcount    43
      Kwlimit      20
      Idlimit      32

  ### File: drcat.pxrf

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     17
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        5
      Fullcount    83
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxsoap

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     18
      Order        71
      Fill         56
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        18
      Fullcount    23
      Kwlimit      15
      Idlimit      32

  ### File: drcat.pxtaxid

      Type         Secondary
      Compress     Yes
      Pages        3
      Secpages     40
      Order        104
      Fill         75
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        26
      Fullcount    114
      Kwlimit      6
      Idlimit      32

  ### File: drcat.pxurl

      Type         Secondary
      Compress     Yes
      Pages        11
      Secpages     268
      Order        52
      Fill         44
      Level        0
      Pagesize     2048
      Cachesize    2000
      Order2       10
      Fill2        13
      Secpagesize  512
      Seccachesize 2000
      Count        227
      Fullcount    585
      Kwlimit      25
      Idlimit      32

  ### File: drcat.xac

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xcat

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xde

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xedat

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xefmt

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xeid

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xetpc

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xid

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xnm

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xqfmt

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xqin

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xqout

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xqurl

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xrest

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xrf

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xsoap

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xtaxid

  This file contains non-printing characters and so cannot be displayed here.

  ### File: drcat.xurl

  This file contains non-printing characters and so cannot be displayed here.

  ### File: outfile.dbxresource

      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'.

  ## Data files

  None.

  ## Notes

  None.

  ## References

  None.

  ## Warnings

  None.

  ## Diagnostic Error Messages

  None.

  ## Exit status

  It always exits with status 0.

  ## Known bugs

  None.

  ## See also

  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

  ## Author(s)

  Peter Rice
  European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

  Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

  ## History

  ## Target users

  This program is intended to be used by administrators responsible for software and database installation and maintenance.

  ## Comments

  None