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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
Database name: EMBL
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GENBANK : Genbank, DDBJ
PIR : NBRF
Entry format [EMBL]: EMBL
Database directory [.]: embl
Wildcard database filename [*.seq]:
Release number [0.0]:
Index date [00/00/00]:
General log output file [outfile.dbigcg]:
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 [EMBL] 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)
-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 [*.dbigcg] 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 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
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: 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.dbigcg
########################################
# Program: dbigcg
# Rundate: Sun 15 Jul 2007 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/07
# CurrentDirectory: /homes/user/test/qa/dbigcg-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbigcg-ex-keep/
# Maxindex: 0
# Fields: 2
# Field 1: id
# Field 2: acc
# Directory: /homes/user/test/embl/
# DirectoryPath: /homes/user/test/embl/
# Filenames: *.seq
# Exclude:
# Files: 9
# File 1: /homes/user/test/embl/eem_ba1.seq
# File 2: /homes/user/test/embl/eem_est.seq
# File 3: /homes/user/test/embl/eem_fun.seq
# File 4: /homes/user/test/embl/eem_htginv1.seq
# File 5: /homes/user/test/embl/eem_hum1.seq
# File 6: /homes/user/test/embl/eem_in.seq
# File 7: /homes/user/test/embl/eem_ov.seq
# File 8: /homes/user/test/embl/eem_ro.seq
# File 9: /homes/user/test/embl/eem_vi.seq
########################################
# Commandline: dbigcg
# -dbname EMBL
# -idformat EMBL
# -directory ../../embl
########################################
filename: '/homes/user/test/embl/eem_ba1.seq'
id: 10
acc: 14
filename: '/homes/user/test/embl/eem_est.seq'
id: 1
acc: 1
filename: '/homes/user/test/embl/eem_fun.seq'
id: 1
acc: 1
filename: '/homes/user/test/embl/eem_htginv1.seq'
id: 5
acc: 5
filename: '/homes/user/test/embl/eem_hum1.seq'
id: 15
acc: 18
filename: '/homes/user/test/embl/eem_in.seq'
id: 2
acc: 2
filename: '/homes/user/test/embl/eem_ov.seq'
id: 2
acc: 2
filename: '/homes/user/test/embl/eem_ro.seq'
id: 3
acc: 3
filename: '/homes/user/test/embl/eem_vi.seq'
id: 1
acc: 2
Index acc: maxlen 8 items 48
Total 9 files 40 entries (0 duplicates)
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 Database indexing for fasta file databases
dbiflat Index a flat file database
dbxfasta Database b+tree indexing for fasta file databases
dbxflat Database b+tree indexing for flat file databases
dbxgcg Database b+tree indexing for GCG formatted databases
Author(s)
Peter Rice (pmr ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome
Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Target users
This program is intended to be used by administrators responsible for
software and database installation and maintenance.
Comments
None
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