                                   dbiflat



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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.

   The resulting index-file 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

Index a flat file database
Version: EMBOSS:6.6.0.0

   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)
   -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)
   -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)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-directory" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension

   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

   '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: Mon 15 Jul 2013 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/13
# 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
                    dbxcompress   Compress an uncompressed dbx index
                    dbxedam       Index the EDAM ontology using b+tree indices
                    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
                    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)

   Peter            Rice
   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

   Completed        December 1999

Target users

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

Comments

                    None
