dbxedam

 

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Function

Index the EDAM ontology using b+tree indices

Description

dbxedam indexes the EDAM ontology in OBO format, 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.

Related application dbxobo can also index the EDAM input file. dbxedam provides additional index fields for EDAM-specific namespaces and relations.

Usage

Here is a sample session with dbxedam 


% dbxedam 
Index the EDAM ontology using b+tree indices
Basename for index files [edam]: 
Standard database name [edam]: 
Resource name [edamresource]: 
Database directory [.]: 
Wildcard database filename [EDAM*.obo]: 
        id : ID
       acc : Synonym
       nam : Name
       isa : Parent
       des : Description
        ns : Namespace
     hasin : has_input
    hasout : has_output
      isid : is_identifier_of
     isfmt : is_format_of
Index fields [*]: 
Compressed index files [Y]: 
General log output file [outfile.dbxedam]:

Go to the output files for this example

Command line arguments 

Index the EDAM ontology using b+tree indices
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     [edam] 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     [edamresource] Resource name (Any string
                                  from 2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [EDAM*.obo] Wildcard database filename (Any
                                  string)
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (Synonym); nam (Name); isa (Parent); des
                                  (Description); ns (Namespace); hasin
                                  (has_input); hasout (has_output); isid
                                  (is_identifier_of); isfmt (is_format_of))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxedam] 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_]+/ edam
[-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_]+/ edamresource
-directory directory Database directory Directory .
-filenames string Wildcard database filename Any string EDAM*.obo
-fields list Index fields
id (ID)
acc (Synonym)
nam (Name)
isa (Parent)
des (Description)
ns (Namespace)
hasin (has_input)
hasout (has_output)
isid (is_identifier_of)
isfmt (is_format_of)
 *
-[no]compressed boolean Compressed index files Boolean value Yes/No Yes
-outfile outfile General log output file Output file <*>.dbxedam
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

dbxedam reads and indexes the EDAM ontology file in OBO format.

Output file format

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

Output files for usage example

File: outfile.dbxedam

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 80 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'.
Field nam namlen 32 OK. Maximum nam term length was 15 for 'semanticscience'.
Field isa isalen 20 OK. Maximum isa term length was 4 for '0003'.
Field ns nslen 15 OK. Maximum ns term length was 10 for 'identifier'.
Field des deslen 30 OK. Maximum des term length was 17 for 'conceptualisation'.
Field hasin hasinlen 15 OK. Maximum hasin term length was 4 for '0006'.
Field hasout hasoutlen 15 OK. Maximum hasout term length was 4 for '0006'.
Field isid isidlen 15 OK. Maximum isid term length was 4 for '0006'.
Field isfmt isfmtlen 15 OK. Maximum isfmt term length was 4 for '0006'.

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        87
Fill         80
Level        0
Pagesize     8192
Cachesize    20000
Order2       406
Fill2        681
Secpagesize  8192
Seccachesize 20000
Count        143
Fullcount    143
Kwlimit      80
Reffiles     0

File: edam.pxde

Type         Secondary
Compress     Yes
Pages        14
Secpages     562
Order        93
Fill         80
Level        0
Pagesize     4096
Cachesize    20000
Order2       144
Fill2        204
Secpagesize  4096
Seccachesize 20000
Count        562
Fullcount    2167
Kwlimit      30
Idlimit      15

File: edam.pxhasin

Type         Secondary
Compress     Yes
Pages        3
Secpages     2
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        2
Fullcount    2
Kwlimit      15
Idlimit      15

File: edam.pxhasout

Type         Secondary
Compress     Yes
Pages        3
Secpages     2
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        2
Fullcount    2
Kwlimit      15
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        60
Fill         49
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        90
Fullcount    225
Kwlimit      20
Idlimit      15

File: edam.pxisfmt

Type         Secondary
Compress     Yes
Pages        3
Secpages     5
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        5
Fullcount    5
Kwlimit      15
Idlimit      15

File: edam.pxisid

Type         Secondary
Compress     Yes
Pages        3
Secpages     1
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        1
Fullcount    1
Kwlimit      15
Idlimit      15

File: edam.pxnm

Type         Secondary
Compress     Yes
Pages        11
Secpages     331
Order        44
Fill         38
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        323
Fullcount    725
Kwlimit      32
Idlimit      15

File: edam.pxns

Type         Secondary
Compress     Yes
Pages        3
Secpages     12
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        5
Fullcount    143
Kwlimit      15
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.xhasin

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

File: edam.xhasout

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.xisfmt

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

File: edam.xisid

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

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
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
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