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dbxgcg |
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A GCG-format database consists of *.seq and *.ref files. The data in the *.seq files is often compressed.
These indexes allow access of flat files larger than 2Gb.
% 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]:
Compressed index files [Y]:
General log output file [outfile.dbxgcg]:
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Go to the output files for this example
Index a GCG formatted database using b+tree indices
Version: EMBOSS:6.5.6.0
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)
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description); key (Keywords); org
(Taxonomy))
-[no]compressed boolean [Y] Compressed index files
-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)
-statistics boolean [N] Report I/O statistics for each input
file
-indexoutdir outdir [.] Index file output directory
Associated qualifiers:
"-directory" associated qualifiers
-extension string Default file extension
"-indexoutdir" associated qualifiers
-extension string Default file extension
"-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 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
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| Qualifier | Type | Description | Allowed values | Default | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||
| [-dbname] (Parameter 1) |
string | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| [-dbresource] (Parameter 2) |
string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| -idformat | list | Entry format |
|
SWISS | ||||||||||||
| -directory | directory | Database directory | Directory | . | ||||||||||||
| -filenames | string | Wildcard database filename | Any string | *.seq | ||||||||||||
| -fields | list | Index fields |
|
id,acc | ||||||||||||
| -[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes | ||||||||||||
| -outfile | outfile | General log output file | Output file | <*>.dbxgcg | ||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||
| (none) | ||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||
| -release | string | Release number | Any string up to 9 characters | 0.0 | ||||||||||||
| -date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||
| -exclude | string | Wildcard filename(s) to exclude | Any string | |||||||||||||
| -statistics | boolean | Report I/O statistics for each input file | Boolean value Yes/No | No | ||||||||||||
| -indexoutdir | outdir | Index file output directory | Output directory | . | ||||||||||||
| Associated qualifiers | ||||||||||||||||
| "-directory" associated directory qualifiers | ||||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||||
| "-indexoutdir" associated outdir qualifiers | ||||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||||
| "-outfile" associated outfile qualifiers | ||||||||||||||||
| -odirectory | string | Output directory | 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 | ||||||||||||
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 Entry idlen 15 OK. Maximum ID length was 8 for 'AB009602'. Field acc acclen 15 OK. Maximum acc term length was 8 for 'AB009602'. |
# Number of files: 9 # Release: 0.0 # Date: 00/00/00 Reference 2 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 |
Type Identifier Compress Yes Pages 3 Secpages 0 Order 71 Fill 46 Level 0 Pagesize 2048 Cachesize 2000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 2000 Count 48 Fullcount 48 Kwlimit 15 Reffiles 1 |
Type Identifier Compress Yes Pages 3 Secpages 0 Order 71 Fill 46 Level 0 Pagesize 2048 Cachesize 2000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 2000 Count 40 Fullcount 40 Kwlimit 15 Reffiles 1 |
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
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.
SET PAGESIZE 2048 SET CACHESIZE 200The 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.
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.
| 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 |
| 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 |
| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.