                                 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:6.4.0.0

   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


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
Order     64
Fill      43
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     21
Fullcount 21
Kwlimit   18

       File: drcat.pxcat

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

       File: drcat.pxde

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

       File: drcat.pxedat

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

       File: drcat.pxefmt

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

       File: drcat.pxeid

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

       File: drcat.pxetpc

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

       File: drcat.pxid

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

       File: drcat.pxnm

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

       File: drcat.pxqfmt

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

       File: drcat.pxqin

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

       File: drcat.pxqout

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

       File: drcat.pxqurl

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

       File: drcat.pxrest

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

       File: drcat.pxrf

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

       File: drcat.pxsoap

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

       File: drcat.pxtaxid

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

       File: drcat.pxurl

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

       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

       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
