                                   dbxobo



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Function

   Index an obo ontology using b+tree indices

Description

   dbxobo indexes an ontology in OBO format, and builds EMBOSS B+tree
   format index files.

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

   Related application dbxedam provides additional index fields for
   EDAM-specific namespaces and relations.

Usage

   Here is a sample session with dbxobo


% dbxobo
Index an obo ontology using b+tree indices
Basename for index files: edam
Standard database name [edam]:
Resource name [oboresource]: oboresource
Database directory [.]:
Wildcard database filename [*.obo]: EDAM.obo
        id : ID
       acc : Synonym
       nam : Name
       isa : Parent
       des : Description
        ns : Namespace
Index fields [*]: *
Compressed index files [Y]:
General log output file [outfile.dbxobo]:


   Go to the output files for this example

Command line arguments

Index an obo ontology using b+tree indices
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     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     [oboresource] Resource name (Any string from
                                  2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [*.obo] Wildcard database filename (Any
                                  string)
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (Synonym); nam (Name); isa (Parent); des
                                  (Description); ns (Namespace))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxobo] 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

   dbxobo reads and indexes OBO format ontology files

Output file format

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

  Output files for usage example

  File: outfile.dbxobo

Processing directory: /homes/user/test/data/
Processing file: EDAM.obo entries: 144 (144) time: 0.0s (0.0s)
Total time: 0.0s

  File: edam.ent

# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
EDAM.obo

  File: edam.pxac

Type      Identifier
Compress  Yes
Pages     6
Order     76
Fill      71
Pagesize  16384
Level     0
Cachesize 100
Order2    816
Fill2     818
Count     153
Fullcount 153
Kwlimit   200

  File: edam.pxde

Type      Secondary
Compress  Yes
Pages     1563
Order     76
Fill      59
Pagesize  4096
Level     0
Cachesize 100
Order2    144
Fill2     204
Count     515
Fullcount 1611
Kwlimit   40

  File: edam.pxid

Type      Identifier
Compress  Yes
Pages     7
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     144
Fullcount 144
Kwlimit   15

  File: edam.pxis

Type      Secondary
Compress  Yes
Pages     229
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     75
Fullcount 230
Kwlimit   15

  File: edam.pxnm

Type      Secondary
Compress  Yes
Pages     618
Order     92
Fill      78
Pagesize  8192
Level     0
Cachesize 100
Order2    290
Fill2     408
Count     204
Fullcount 425
Kwlimit   75

  File: edam.pxns

Type      Secondary
Compress  Yes
Pages     21
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     6
Fullcount 144
Kwlimit   20

  File: edam.xac

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

  File: edam.xde

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

  File: edam.xid

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

  File: edam.xis

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

  File: edam.xnm

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

  File: edam.xns

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

Data files

Notes

References

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It exits with a status of 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
                    dbxreport     Validate index and report internals for dbx databases
                    dbxresource   Index a data resource catalogue using b+tree indices
                    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
