EMBOSS: dbigcg

dbigcg

Wiki

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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. The data in the *.seq files 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.

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

Index a GCG formatted database
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [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)
   -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)
   -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

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-dbname]
(Parameter 1) string Database name Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required

-idformat list Entry format
EMBL (EMBL)
SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew)
GENBANK (Genbank, DDBJ)
PIR (NBRF)
EMBL

-directory directory Database directory Directory .

-filenames string Wildcard database filename Any string *.seq

-release string Release number Any string up to 9 characters 0.0

-date string Index date Date string dd/mm/yy 00/00/00

-outfile outfile General log output file Output file <*>.dbigcg

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

-fields list Index fields
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)
acc

-exclude string Wildcard filename(s) to exclude Any string

-maxindex integer Maximum index length Integer 0 or more 0

-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 Any string -T . -k 1,1

-[no]systemsort boolean Use system sort utility Boolean value Yes/No Yes

-[no]cleanup boolean Clean up temporary files Boolean value Yes/No Yes

-indexoutdir outdir Index file output directory Output directory .

Associated qualifiers

"-directory" associated directory qualifiers

-extension string Default file extension Any string

"-outfile" associated outfile qualifiers

-odirectory string Output directory Any string

"-indexoutdir" associated outdir qualifiers

-extension string Default file extension Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

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: Fri 15 Jul 2011 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/11
# 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

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.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0 if no errors.

Known bugs

None.

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

History

Target users

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

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: division.lkp

File: entrynam.idx

File: acnum.hit

File: acnum.trg

File: outfile.dbigcg

Data files

Notes

Fields Indexed

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments