EMBOSS at CSC

Tehdyt toimenpiteet

EMBOSS: dbxedam

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:6.4.0.0

   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

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: 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     4
Order     87
Fill      75
Pagesize  8192
Level     0
Cachesize 100
Order2    406
Fill2     408
Count     153
Fullcount 153
Kwlimit   80

File: edam.pxde

Type      Secondary
Compress  Yes
Pages     1556
Order     93
Fill      69
Pagesize  4096
Level     0
Cachesize 100
Order2    144
Fill2     204
Count     515
Fullcount 1611
Kwlimit   30

File: edam.pxhasin

Type      Secondary
Compress  Yes
Pages     12
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     3
Fullcount 3
Kwlimit   15

File: edam.pxhasout

Type      Secondary
Compress  Yes
Pages     15
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     4
Fullcount 7
Kwlimit   15

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.pxisfmt

Type      Secondary
Compress  Yes
Pages     24
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     7
Fullcount 20
Kwlimit   15

File: edam.pxisid

Type      Secondary
Compress  Yes
Pages     6
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     1
Fullcount 1
Kwlimit   15

File: edam.pxnm

Type      Secondary
Compress  Yes
Pages     622
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    71
Fill2     101
Count     204
Fullcount 425
Kwlimit   20