                                  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)
      idsv : >ID SV or >ID (SV)
     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:6.6.0.0

   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)); idsv
                                  (>ID SV or >ID (SV)); 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)
   -statistics         boolean    [N] Report I/O statistics for each input
                                  file
   -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


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: 0.0/0.0s (-0.0/0.0)
Total time: 0:00.0
Entry idlen 15 OK. Maximum ID length was 6 for 'L48662'.
Field acc acclen 15 OK. Maximum acc term length was 6 for 'L48662'.

  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
Secpages     0
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        6
Fullcount    6
Kwlimit      15
Reffiles     0

  File: emrod.pxid

Type         Identifier
Compress     Yes
Pages        3
Secpages     0
Order        71
Fill         56
Level        0
Pagesize     2048
Cachesize    20000
Order2       22
Fill2        41
Secpagesize  512
Seccachesize 20000
Count        6
Fullcount    6
Kwlimit      15
Reffiles     0

  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 (c) 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
