
                                 dbifasta 



Function

   Index a fasta database

Description

   dbifasta 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.

   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: fasta
   method: emblcd
   directory: /data/embl/fasta
]

  Fields Indexed

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

Usage

   Here is a sample session with dbifasta


% dbifasta 
Index a fasta database
Database name: EMROD
    simple : >ID
     idacc : >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]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name
   -idformat           menu       ID line format
   -directory          directory  Database directory
   -filenames          string     Wildcard database filename
   -release            string     Release number
   -date               string     Index date

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       Index fields
   -exclude            string     Wildcard filename(s) to exclude
   -maxindex           integer    Maximum index length
   -sortoptions        string     Sort options, typically '-T .' to use
                                  current directory for work files and '-k
                                  1,1' to force GNU sort to use the first
                                  field
   -[no]systemsort     boolean    Use system sort utility
   -[no]cleanup        boolean    Clean up temporary files
   -indexoutdir        outdir     Index 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-dbname]
   (Parameter 1) Database name A string from 2 to 19 characters, matching
   regular expression /[A-z][A-z0-9_]+/ Required
   -idformat ID line format
   simple   (>ID)
   idacc    (>ID ACC)
   gcgid    (>db:ID)
   gcgidacc (>db:ID ACC)
   dbid     (>db ID)
   ncbi     (| formats)
   idacc
   -directory Database directory Directory .
   -filenames Wildcard database filename Any string is accepted *.dat
   -release Release number A string up to 9 characters 0.0
   -date Index date Date string dd/mm/yy 00/00/00
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -fields Index fields
   acnum (Accession number)
   seqvn (Sequence Version and GI)
   des   (Description)
   acnum
   -exclude Wildcard filename(s) to exclude Any string is accepted An
   empty string is accepted
   -maxindex Maximum index length Integer 0 or more 0
   -sortoptions 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 -T . -k 1,1
   -[no]systemsort Use system sort utility Boolean value Yes/No Yes
   -[no]cleanup Clean up temporary files Boolean value Yes/No Yes
   -indexoutdir Index directory Output directory .

Input file format

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.

   dbifasta 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.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   Exit status It always exits with status 0.

Known bugs

   None.

See also

   Program name          Description
   dbiblast     Index a BLAST database
   dbiflat      Index a flat file database
   dbigcg       Index a GCG formatted database

Author(s)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Completed August 2000

Target users

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

Comments

   None
