dbxtax

 

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 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 directory Database directory Directory .
-fields list Index fields
id (ID)
acc (Synonym)
tax (Scientific name)
rnk (Rank)
up (Parent)
gc (Genetics code)
mgc (Mitochondrial genetic code)
 *
-[no]compressed boolean Compressed index files Boolean value Yes/No Yes
-outfile outfile General log output file Output file <*>.dbxtax
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
-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

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.