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EMBOSS: dbxfasta
dbxfasta

 

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Function

Index a fasta file database using b+tree indices

Description

dbxfasta indexes a flat file database of one or more 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 dbxfasta 


% dbxfasta 
Index a fasta file database using b+tree indices
Basename for index files: emrod
Resource name: emblresource
    simple : >ID
     idacc : >ID ACC or >ID (ACC)
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      dbid : >db ID
      ncbi : | formats
ID line format [idacc]: idacc
Database directory [.]: data
Wildcard database filename [*.fasta]: emrod
        id : ID
       acc : Accession number
        sv : Sequence Version and GI
       des : Description
Index fields [id,acc]: 
Compressed index files [Y]: 
General log output file [outfile.dbxfasta]:

Go to the output files for this example

Command line arguments 

Index a fasta file database using b+tree indices
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Basename for index files (Any string from 2
                                  to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     Resource name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [idacc] ID line format (Values: simple
                                  (>ID); idacc (>ID ACC or >ID (ACC)); gcgid
                                  (>db:ID); gcgidacc (>db:ID ACC); dbid (>db
                                  ID); ncbi (| formats))
   -directory          directory  [.] Database directory
   -filenames          string     [*.fasta] Wildcard database filename (Any
                                  string)
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxfasta] 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_]+/ Required
[-dbresource]
(Parameter 2)		 string Resource name Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required
-idformat list ID line format
simple (>ID)
idacc (>ID ACC or >ID (ACC))
gcgid (>db:ID)
gcgidacc (>db:ID ACC)
dbid (>db ID)
ncbi (| formats)
 idacc
-directory directory Database directory Directory .
-filenames string Wildcard database filename Any string *.fasta
-fields list Index fields
id (ID)
acc (Accession number)
sv (Sequence Version and GI)
des (Description)
 id,acc
-[no]compressed boolean Compressed index files Boolean value Yes/No Yes
-outfile outfile General log output file Output file <*>.dbxfasta
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

dbxfasta reads and indexes FASTA format sequence data files.

Output file format

dbxfasta 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.dbxfasta

Processing directory: /homes/user/test/data/
Processing file: emrod entries: 6 (6) time: 0.0s (0.0s)
Total time: 0.0s

File: emrod.ent

# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
emrod

File: emrod.pxac

Type      Identifier
Compress  Yes
Pages     3
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     6
Fullcount 6
Kwlimit   15

File: emrod.pxid

Type      Identifier
Compress  Yes
Pages     3
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     6
Fullcount 6
Kwlimit   15

File: emrod.xac

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

File: emrod.xid

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

Data files

None.

Notes

The indexing system has been designed to allow on-the-fly updating of indexes. This feature is, however, not implemented in the current version. It will be made available in future releases.

Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like: 

DB emrod [
   type: N
   dbalias: emrod   (see below)
   format: fasta
   method: emboss
   directory: /data/embl/fasta
   file: emrod.fasta
   indexdirectory: /data/embl/fasta/indexes
]
The index file 'basename' given to dbxfasta must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.

Fields Indexed

By default, dbxfasta will index the ID name and the accession number (if present).
If they are present in your database, you may also specify that dbxfasta should index the Sequence Version and GI, the words in the description, the keywords and the organism words using the '-fields' qualifier with the appropriate values.

Global Parameters

dbxfasta requires that two global parameters be defined in the file emboss.defaults. These are: 
SET PAGESIZE 2048
SET CACHESIZE 200
The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxfasta is allowed to cache.

Resources

dbxfasta will ask you for the name of a resource definition in the file emboss.defaults. This will be something like: 
RES embl [
   type: Index
   idlen:  15
   acclen: 15
   svlen:  20
   keylen: 25
   deslen: 25
   orglen: 25
]
The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set.

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
dbxedam Index the EDAM ontology 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)

Alan Bleasby
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