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EMBOSS: dbxresource
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

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
    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 © 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