EMBOSS: dbxgcg

dbxgcg

Function

Index a GCG formatted database using b+tree indices

Description

dbxgcg indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

Usage

Here is a sample session with dbxgcg

% dbxgcg Index a GCG formatted database using b+tree indices Basename for index files: embl Resource name: emblresource EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GENBANK : Genbank, DDBJ PIR : NBRF Entry format [SWISS]: embl Database directory [.]: embl Wildcard database filename [*.seq]: id : ID acc : Accession number sv : Sequence Version and GI des : Description key : Keywords org : Taxonomy Index fields [id,acc]: General log output file [outfile.dbxgcg]:

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Basename for index files (Any string from 2
                                  to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     Resource 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);
                                  GENBANK (Genbank, DDBJ); PIR (NBRF))
   -directory          directory  [.] Database directory
   -filenames          string     [*.seq] Wildcard database filename (Any
                                  string is accepted)
   -fields             menu       [id,acc] Index fields (Values: id (ID); acc
                                  (Accession number); sv (Sequence Version and
                                  GI); des (Description); key (Keywords); org
                                  (Taxonomy))
   -outfile            outfile    [*.dbxgcg] General log output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -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 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. 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

Standard (Mandatory) qualifiers Allowed values Default

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

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

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

-directory Database directory Directory .

-filenames Wildcard database filename Any string is accepted *.seq

-fields Index fields
id (ID)
acc (Accession number)
sv (Sequence Version and GI)
des (Description)
key (Keywords)
org (Taxonomy)
id,acc

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

Additional (Optional) qualifiers Allowed values Default

(none)

Advanced (Unprompted) qualifiers Allowed values Default

-release Release number Any string up to 9 characters 0.0

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

-exclude Wildcard filename(s) to exclude Any string is accepted An empty string is accepted

-indexoutdir Index file output directory Output directory .

Input file format

dbxgcg reads any normal sequence USAs.

Output file format

dbxgcg creates one summary file for the database and two files for each field indexed.

dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
dbalias.xid is the B+tree index file for the ID names. It is a binary file.
dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

Output files for usage example

File: outfile.dbxgcg

Processing directory: /homes/user/test/embl/
Processing file: eem_ba1.seq entries: 10 (10) time: 0.0s (0.0s)
Processing file: eem_est.seq entries: 11 (1) time: 0.0s (0.0s)
Processing file: eem_fun.seq entries: 12 (1) time: 0.0s (0.0s)
Processing file: eem_htginv1.seq entries: 17 (5) time: 0.0s (0.0s)
Processing file: eem_hum1.seq entries: 32 (15) time: 0.0s (0.0s)
Processing file: eem_in.seq entries: 34 (2) time: 0.0s (0.0s)
Processing file: eem_ov.seq entries: 36 (2) time: 0.0s (0.0s)
Processing file: eem_ro.seq entries: 39 (3) time: 0.0s (0.0s)
Processing file: eem_vi.seq entries: 40 (1) time: 0.0s (0.0s)
Total time: 0.0s

File: embl.ent

# Number of files: 9
# Release: 0.0
# Date:    00/00/00
Dual filename database
eem_ba1.seq eem_ba1.ref
eem_est.seq eem_est.ref
eem_fun.seq eem_fun.ref
eem_htginv1.seq eem_htginv1.ref
eem_hum1.seq eem_hum1.ref
eem_in.seq eem_in.ref
eem_ov.seq eem_ov.ref
eem_ro.seq eem_ro.ref
eem_vi.seq eem_vi.ref

File: embl.pxac

Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     47
Kwlimit   15

File: embl.pxid

Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     39
Kwlimit   15

File: embl.xac

This file contains non-printing characters and so cannot be displayed here.

File: embl.xid

This file contains non-printing characters and so cannot be displayed here.

Data files

None.

Notes

The indexing system has been designed to allow on-the-fly updating of indexes. This feature is, however, not implemented in the current version. It will be made available in future releases.

Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like:

DB embl [
   type: N
   dbalias: embl   (see below)
   format: embl
   method: embossgcg
   directory: /data/gcg/embl
   file: *.seq
   indexdirectory: /data/gcg/embl/indexes
]

The index file 'basename' given to dbxgcg must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.

Fields Indexed

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

Global Parameters

dbxgcg requires that two global parameters be defined in the file emboss.defaults. These are:

SET PAGESIZE 2048
SET CACHESIZE 200

The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxgcg is allowed to cache.

Resources

dbxgcg will ask you for the name of a resource definition in the file emboss.defaults. This will be something like:

RES embl [
   type: Index
   idlen:  15
   acclen: 15
   svlen:  20
   keylen: 25
   deslen: 25
   orglen: 25
]

The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
dbiblast	Index a BLAST database
dbifasta	Index a fasta file database
dbiflat	Index a flat file database
dbigcg	Index a GCG formatted database
dbxfasta	Index a fasta file database using b+tree indices
dbxflat	Index a flat file database using b+tree indices

Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Function

Description

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: outfile.dbxgcg

File: embl.ent

File: embl.pxac

File: embl.pxid

File: embl.xac

File: embl.xid

Data files

Notes

Fields Indexed

Global Parameters

Resources

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments