
                                  dbigcg 
                                      
   
   
Function

   Index a GCG formatted database
   
Description

   dbigcg indexes a GCG-format database of one or more files, and builds
   EMBL CD-ROM format index files.
   
   A GCG-format database consists of *.seq and *.ref files - only the
   *.seq files are used. The data in these is often compressed.
   
   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.
   
   Having created the EMBOSS indices for this file, a database can then
   be defined in the file emboss.defaults as something like:
   
DB embl [
   type: N
   format: embl
   method: gcg
   directory: /data/gcg/gcgembl
]

  Fields Indexed
  
   By default, dbigcg will index the ID name and the accession number (if
   present).
   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.
   
Usage

   Here is a sample session with dbigcg
   

% dbigcg 
Index a GCG formatted database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
   GENBANK : Genbank, DDBJ
       PIR : NBRF
Entry format [EMBL]: EMBL
Database directory [.]: ../../embl
Wildcard database filename [*.seq]: 
Database name: EMBL
Release number [0.0]: 
Index date [00/00/00]: 
   
   Go to the output files for this example
   
Command line arguments

   Standard (Mandatory) qualifiers:
   -idformat           menu       Entry format
   -directory          directory  Database directory
   -filenames          string     Wildcard database filename
  [-dbname]            string     Database name
   -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
   -indexdirectory     directory  Index directory
   -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

   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
   -idformat Entry format
   EMBL    (EMBL)
   SWISS   (Swiss-Prot, SpTrEMBL, TrEMBLnew)
   GENBANK (Genbank, DDBJ)
   PIR     (NBRF)
   EMBL
   -directory Database directory Directory .
   -filenames Wildcard database filename Any string is accepted *.seq
   [-dbname]
   (Parameter 1) Database name A string from 1 to 19 characters Required
   -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)
   keyword (Keywords)
   taxon   (Taxonomy)
   acnum
   -exclude Wildcard filename(s) to exclude Any string is accepted An
   empty string is accepted
   -indexdirectory Index directory Directory .
   -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
   
Input file format

   dbigcg reads in a GCG-format database. A GCG-format database consists
   of *.seq and *.ref files - only the *.seq files are used. The data in
   these is often compressed.
   
Output file format

  Output files for usage example
  
  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: 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.
   
   dbigcg 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 names for the reference file
       and 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

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It exits with a status of 0 if no errors.
   
Known bugs

   None.
   
See also

   Program name        Description
   dbiblast     Index a BLAST database
   dbifasta     Index a fasta database
   dbiflat      Index a flat file database
   
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
