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EMBOSS: dbxtax

dbxtax

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Function

Index NCBI taxonomy using b+tree indices

Description

dbxflat indexes NCBI taxonomy files, and builds EMBOSS B+tree format index files.

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

Usage

Here is a sample session with dbxtax


% dbxtax 
Index NCBI taxonomy using b+tree indices
Basename for index files [taxon]: 
Resource name [taxresource]: 
Database directory [.]: taxonomy
        id : ID
       acc : Synonym
       tax : Scientific name
       rnk : Rank
        up : Parent
        gc : Genetics code
       mgc : Mitochondrial genetic code
Index fields [*]: 
Compressed index files [Y]: 
General log output file [outfile.dbxtax]:

Go to the output files for this example

Command line arguments

Index NCBI taxonomy using b+tree indices
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     [taxon] Basename for index files (Any string
                                  from 2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     [taxresource] Resource name (Any string from
                                  2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (Synonym); tax (Scientific name); rnk
                                  (Rank); up (Parent); gc (Genetics code); mgc
                                  (Mitochondrial genetic code))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxtax] 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)
   -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_]+/

taxon

[-dbresource]
(Parameter 2)

string

Resource name

Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/

taxresource

-directory

Input file format

dbxtax reads and indexes the NCBI taxonomy nodes.dmp, names.dmp, division.dmp, gencode.dmp,and merged.dmp files.

Output file format

dbxtax 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.dbxtax

Processing directory: /homes/user/test/data/taxonomy/
Processing file: nodes.dmp entries: 41 (41) time: 0.0s (0.0s)
Total time: 0.0s

File: taxon.ent

# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Dual filename database
nodes.dmp names.dmp

File: taxon.pxac

Type      Identifier
Compress  Yes
Pages     3
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     1
Fullcount 1
Kwlimit   15

File: taxon.pxgc

Type      Secondary
Compress  Yes
Pages     6
Order     132
Fill      65
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     169
Count     1
Fullcount 41
Kwlimit   2

File: taxon.pxid

Type      Identifier
Compress  Yes
Pages     3
Order     99
Fill      56
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     41
Fullcount 41
Kwlimit   7

File: taxon.pxmgc

Type      Secondary
Compress  Yes
Pages     12
Order     132
Fill      65
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     169
Count     3
Fullcount 39
Kwlimit   2

File: taxon.pxtax

Type      Identifier
Compress  Yes
Pages     19
Order     16
Fill      14
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     86
Fullcount 90
Kwlimit   110

File: taxon.pxrnk

Type      Secondary
Compress  Yes
Pages     54
Order     68
Fill      45
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     169
Count     17
Fullcount 41
Kwlimit   16