                                 dbxresource



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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


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 cla
ssification 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 (t
ranscription 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 'identificationAcc
essionNumber'.
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 'prideMartWebServi
ce'.
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 (c) 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
