dbxedam |
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These indexes allow access of flat files larger than 2Gb.
Related application dbxobo can also index the EDAM input file. dbxedam provides additional index fields for EDAM-specific namespaces and relations.
% dbxedam Index the EDAM ontology using b+tree indices Basename for index files [edam]: Standard database name [edam]: Resource name [edamresource]: Database directory [.]: Wildcard database filename [EDAM*.obo]: id : ID acc : Synonym nam : Name isa : Parent des : Description ns : Namespace hasin : has_input hasout : has_output isid : is_identifier_of isfmt : is_format_of Index fields [*]: Compressed index files [Y]: General log output file [outfile.dbxedam]: |
Go to the output files for this example
Index the EDAM ontology using b+tree indices Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string [edam] Basename for index files (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-standardname] string [$(dbname)] Standard database name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-dbresource] string [edamresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -filenames string [EDAM*.obo] Wildcard database filename (Any string) -fields menu [*] Index fields (Values: id (ID); acc (Synonym); nam (Name); isa (Parent); des (Description); ns (Namespace); hasin (has_input); hasout (has_output); isid (is_identifier_of); isfmt (is_format_of)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxedam] 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) -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 |
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_]+/ | edam | ||||||||||||||||||||
[-standardname] (Parameter 2) |
string | Standard database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | $(dbname) | ||||||||||||||||||||
[-dbresource] (Parameter 3) |
string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | edamresource | ||||||||||||||||||||
-directory | directory | Database directory | Directory | . | ||||||||||||||||||||
-filenames | string | Wildcard database filename | Any string | EDAM*.obo | ||||||||||||||||||||
-fields | list | Index fields |
|
* | ||||||||||||||||||||
-[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes | ||||||||||||||||||||
-outfile | outfile | General log output file | Output file | <*>.dbxedam | ||||||||||||||||||||
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 | |||||||||||||||||||||
-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/data/ Processing file: EDAM.obo entries: 144 (144) time: 0.0s (0.0s) Total time: 0.0s |
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database EDAM.obo |
Type Identifier Compress Yes Pages 4 Order 87 Fill 75 Pagesize 8192 Level 0 Cachesize 100 Order2 406 Fill2 408 Count 153 Fullcount 153 Kwlimit 80 |
Type Secondary Compress Yes Pages 1556 Order 93 Fill 69 Pagesize 4096 Level 0 Cachesize 100 Order2 144 Fill2 204 Count 515 Fullcount 1611 Kwlimit 30 |
Type Secondary Compress Yes Pages 12 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 3 Fullcount 3 Kwlimit 15 |
Type Secondary Compress Yes Pages 15 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 4 Fullcount 7 Kwlimit 15 |
Type Identifier Compress Yes Pages 7 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 144 Fullcount 144 Kwlimit 15 |
Type Secondary Compress Yes Pages 229 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 75 Fullcount 230 Kwlimit 15 |
Type Secondary Compress Yes Pages 24 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 7 Fullcount 20 Kwlimit 15 |
Type Secondary Compress Yes Pages 6 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 1 Fullcount 1 Kwlimit 15 |
Type Secondary Compress Yes Pages 622 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 204 Fullcount 425 Kwlimit 20 |
Type Secondary Compress Yes Pages 21 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 6 Fullcount 144 Kwlimit 15 |
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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 |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.