
                                  dbxgcg 



Function

   Database b+tree indexing for GCG formatted databases

Description

   dbxgcg 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 embl [
   type: N
   dbalias: embl   (see below)
   format: embl
   method: embossgcg
   directory: /data/gcg/embl
   file: *.seq
   indexdirectory: /data/gcg/embl/indexes
]

   The index file 'basename' given to dbxgcg 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, dbxgcg will index the ID name and the accession number (if
   present).
   If they are present in your database, you may also specify that dbxgcg
   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 dbxgcg


% dbxgcg 
Database b+tree indexing for GCG formatted databases
Basename for index files: embl
Resource name: embl
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
   GENBANK : Genbank, DDBJ
       PIR : NBRF
Entry format [SWISS]: embl
Database directory [.]: embl
Wildcard database filename [*.seq]: 
        id : ID
       acc : Accession number
        sv : Sequence Version and GI
       des : Description
       key : Keywords
       org : Taxonomy
Index fields [id,acc]: 

Processing file /homes/user/test/embl/eem_ba1.seq
Processing file /homes/user/test/embl/eem_est.seq
Processing file /homes/user/test/embl/eem_fun.seq
Processing file /homes/user/test/embl/eem_htginv1.seq
Processing file /homes/user/test/embl/eem_hum1.seq
Processing file /homes/user/test/embl/eem_in.seq
Processing file /homes/user/test/embl/eem_ov.seq
Processing file /homes/user/test/embl/eem_ro.seq
Processing file /homes/user/test/embl/eem_vi.seq

   Go to the output files for this example

Global Parameters

   dbxgcg 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 dbxgcg is allowed to cache.

Resources

   dbxgcg 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       [SWISS] Entry format (Values: EMBL (EMBL);
                                  SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew);
                                  GENBANK (Genbank, DDBJ); PIR (NBRF))
   -directory          directory  [.] Database directory
   -filenames          string     [*.seq] Wildcard database filename (Any
                                  string is accepted)
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description); key (Keywords); org
                                  (Taxonomy))

   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
                                  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

   dbxgcg reads any normal sequence USAs.

Output file format

   dbxgcg 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: embl.ent

# Number of files: 9
# Release: 0.0
# Date:    00/00/00
Dual filename database
eem_ba1.seq eem_ba1.ref
eem_est.seq eem_est.ref
eem_fun.seq eem_fun.ref
eem_htginv1.seq eem_htginv1.ref
eem_hum1.seq eem_hum1.ref
eem_in.seq eem_in.ref
eem_ov.seq eem_ov.ref
eem_ro.seq eem_ro.ref
eem_vi.seq eem_vi.ref

  File: embl.pxac

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

  File: embl.pxid

Order     71
Fill      47
Pagesize  2048
Level     0
Cachesize 200
Order2    82
Fill2     99
Count     39
Kwlimit   15

  File: embl.xac

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

  File: embl.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
   dbxfasta     Database b+tree indexing for fasta file databases
   dbxflat      Database b+tree indexing for flat file 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
