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:6.6.0.0

   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

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_]+/ Required
[-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_]+/ oboresource
-directory directory Database directory Directory .
-filenames string Wildcard database filename Any string *.obo
-fields list Index fields
id (ID)
acc (Synonym)
nam (Name)
isa (Parent)
des (Description)
ns (Namespace)
 *
-[no]compressed boolean Compressed index files Boolean value Yes/No Yes
-outfile outfile General log output file Output file <*>.dbxobo
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

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: 143 (143) time: 0.0s (0.0s)
Total time: 0.0s
Entry idlen 15 OK. Maximum ID length was 4 for '0004'.
Field acc acclen 200 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'.
Field nam namlen 70 OK. Maximum nam term length was 15 for 'semanticscience'.
Field isa isalen 15 OK. Maximum isa term length was 4 for '0003'.
Field ns nslen 20 OK. Maximum ns term length was 10 for 'identifier'.
Field des deslen 50 OK. Maximum des term length was 17 for 'conceptualisation'.

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        3
Secpages     0
Order        76
Fill         74
Level        0
Pagesize     16384
Cachesize    20000
Order2       816
Fill2        1364
Secpagesize  16384
Seccachesize 20000
Count        143
Fullcount    143
Kwlimit      200
Reffiles     0

File: edam.pxde

Type         Secondary
Compress     Yes
Pages        21
Secpages     562
Order        64
Fill         57
Level        0
Pagesize     4096
Cachesize    20000
Order2       144
Fill2        204
Secpagesize  4096
Seccachesize 20000
Count        562
Fullcount    2167
Kwlimit      50
Idlimit      15

File: edam.pxid

Type         Identifier
Compress     Yes
Pages        5
Secpages     0
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        143
Fullcount    143
Kwlimit      15
Reffiles     0

File: edam.pxis

Type         Secondary
Compress     Yes
Pages        4
Secpages     96
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        90
Fullcount    225
Kwlimit      15
Idlimit      15

File: edam.pxnm

Type         Secondary
Compress     Yes
Pages        5
Secpages     323
Order        196
Fill         179
Level        0
Pagesize     16384
Cachesize    20000
Order2       583
Fill2        818
Secpagesize  16384
Seccachesize 20000
Count        323
Fullcount    725
Kwlimit      70
Idlimit      15

File: edam.pxns

Type         Secondary
Compress     Yes
Pages        3
Secpages     12
Order        60
Fill         49
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        5
Fullcount    143
Kwlimit      20
Idlimit      15

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 © 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