                                   dbxedam



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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


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.

     * 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: 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 alignm
ent (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 (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
