
                                 dbxfasta 



Function

   Database b+tree indexing for fasta file databases

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.

   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.

Usage

   Here is a sample session with dbxfasta


% dbxfasta 
Database b+tree indexing for fasta file databases
Basename for index files: emrod
Resource name: embl
    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 [*.dat]: emrod
Release number [0.0]: 
Index date [00/00/00]: 

Processing file /homes/user/test/data/emrod

   Go to the output files for this example

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.

Command line arguments

   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     [*.dat] Wildcard database filename (Any
                                  string is accepted)
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description))
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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

Input file format

   dbxfasta reads any normal sequence USAs.

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: emrod.ent

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

  File: emrod.pxac

Order     71
Fill      47
Pagesize  2048
Level     0
Cachesize 200
Order2    82
Fill2     99
Count     5
Kwlimit   15

  File: emrod.pxid

Order     71
Fill      47
Pagesize  2048
Level     0
Cachesize 200
Order2    82
Fill2     99
Count     5
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.

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     Database indexing for fasta file databases
   dbiflat      Index a flat file database
   dbigcg       Index a GCG formatted database
   dbxflat      Database b+tree indexing for flat file databases
   dbxgcg       Database b+tree indexing for GCG formatted databases

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
