
                                  dbiflat 



Function

   Index a flat file database

Description

   dbiflat indexes a flat file database of one or more files, and builds
   EMBL CD-ROM format index files. This format is used by the software on
   the EMBL database CD-ROM distribution and by the Staden package in
   addition to EMBOSS, and appears to be the most generally used and
   publicly available index file format for these databases.

   A flat file database is a database in one of the native formats: EMBL,
   Swiss-Prot or GenBank, as distributed by the EBI, NCBI, or DDBJ. (It
   is called a 'flat' file to distinguish it from the complex relational
   database formats that this data is held in before being written to
   files and distributed.)

Usage

   Here is a sample session with dbiflat


% dbiflat 
Index a flat file database
Database name: EMBL
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]: EMBL
Database directory [.]: embl
Wildcard database filename [*.dat]: rod.dat
Release number [0.0]: 
Index date [00/00/00]: 
General log output file [outfile.dbiflat]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database 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); GB
                                  (Genbank, DDBJ); REFSEQ (Refseq))
   -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)
   -outfile            outfile    [*.dbiflat] General log output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       [acc] Index fields (Values: acc (acnum
                                  accession number index); sv (seqvn sequence
                                  version and gi number index); des (des
                                  description index); key (keyword keywords
                                  index); org (taxon taxonomy and organism
                                  index))
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -maxindex           integer    [0] Maximum index length (Integer 0 or more)
   -sortoptions        string     [-T . -k 1,1] Sort options, typically '-T .'
                                  to use current directory for work files and
                                  '-k 1,1' to force GNU sort to use the first
                                  field (Any string is accepted)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-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. 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

   'flat' files (native distribution format) of a protein or nucleic
   sequence database.

Output file format

  Output files for usage example

  File: division.lkp

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

  File: entrynam.idx

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

  File: acnum.hit

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

  File: acnum.trg

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

  File: outfile.dbiflat

########################################
# Program: dbiflat
# Rundate: Tue 15 Jul 2008 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/08
# CurrentDirectory: /homes/user/test/qa/dbiflat-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiflat-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/embl/
# DirectoryPath: /homes/user/test/embl/
# Filenames: rod.dat
# Exclude:
# Files: 1
#   File 1: /homes/user/test/embl/rod.dat
########################################
# Commandline: dbiflat
#    -dbname EMBL
#    -idformat EMBL
#    -directory ../../embl
#    -filenames rod.dat
########################################

filename: 'rod.dat'
    id: 6
   acc: 9

Index acc: maxlen 6 items 7

Total 1 files 6 entries (0 duplicates)

   dbiflat creates four index files. All are binary but with a simple
   format.
     * division.lkp is the master index file, and has a 300 byte header
       containing the database name and date plus information on the
       record size. This header is followed by one record for each
       database file, giving the full file name for the data file, and
       optionally a second sequence file.
     * entryname.idx is the entry name index. It has the same 300 byte
       header, mainly used to store the record size which will depend on
       the size of the longest entryname in the database. Each entry is
       stored in sorted alphanumeric order so that a binary search can be
       used to efficiently find any record. The record also holds the
       file number from division.lkp and the offsets in the data and
       sequence files for that entry.
     * acnum.trg holds the accession number information. The file has the
       usual 300 byte header, and a sorted list of record by accession
       number. Each accession number record contains the first record
       number in acnum.hit and the total number of records in acnum.hit
       so that secondary (duplicated) accession numbers can be searched.
     * acnum.hit is a very simple file. After the usual 300 byte header,
       each record simply holds the record number in entryname.idx. An
       accession number search will use acnum.trg to find a start
       position and number of records to read in this file, and will then
       simply read the entryname.idx records for each entry in turn.

Data files

   None.

Notes

   The indexing method depends on each entry having a unique entry name.
   No allowance is made for two entries with the same name so it is not
   possible to index EMBL and EMBLNEW together.

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

DB emrod [
   type: N
   format: embl
   method: emblcd
   directory: /data/embl
]

  Fields Indexed

   By default, dbiflat will index the ID name and the accession number.
   If they are present in your database, you may also specify that
   dbiflat should index the Sequence Version and GI number, the Keywords
   and Taxonomy names and the words in the description by using the
   '-fields' qualifier with the appropriate values.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It exits with a status of 0 if no problems.

Known bugs

   None.

See also

   Program name                     Description
   dbiblast     Index a BLAST database
   dbifasta     Index a fasta file database
   dbigcg       Index a GCG formatted database
   dbxfasta     Index a fasta file database using b+tree indices
   dbxflat      Index a flat file database using b+tree indices
   dbxgcg       Index a GCG formatted database using b+tree indices

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Completed December 1999

Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.

Comments

   None
