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:6.6.0.0 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: 143 (143) time: 0.0s (0.0s) Total time: 0.0s Entry idlen 15 OK. Maximum ID length was 4 for '0004'. Field acc acclen 80 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'. Field nam namlen 32 OK. Maximum nam term length was 15 for 'semanticscience'. Field isa isalen 20 OK. Maximum isa term length was 4 for '0003'. Field ns nslen 15 OK. Maximum ns term length was 10 for 'identifier'. Field des deslen 30 OK. Maximum des term length was 17 for 'conceptualisation'. Field hasin hasinlen 15 OK. Maximum hasin term length was 4 for '0006'. Field hasout hasoutlen 15 OK. Maximum hasout term length was 4 for '0006'. Field isid isidlen 15 OK. Maximum isid term length was 4 for '0006'. Field isfmt isfmtlen 15 OK. Maximum isfmt term length was 4 for '0006'. |
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database EDAM.obo |
Type Identifier Compress Yes Pages 3 Secpages 0 Order 87 Fill 80 Level 0 Pagesize 8192 Cachesize 20000 Order2 406 Fill2 681 Secpagesize 8192 Seccachesize 20000 Count 143 Fullcount 143 Kwlimit 80 Reffiles 0 |
Type Secondary Compress Yes Pages 14 Secpages 562 Order 93 Fill 80 Level 0 Pagesize 4096 Cachesize 20000 Order2 144 Fill2 204 Secpagesize 4096 Seccachesize 20000 Count 562 Fullcount 2167 Kwlimit 30 Idlimit 15 |
Type Secondary Compress Yes Pages 3 Secpages 2 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 2 Fullcount 2 Kwlimit 15 Idlimit 15 |
Type Secondary Compress Yes Pages 3 Secpages 2 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 2 Fullcount 2 Kwlimit 15 Idlimit 15 |
Type Identifier Compress Yes Pages 5 Secpages 0 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 143 Fullcount 143 Kwlimit 15 Reffiles 0 |
Type Secondary Compress Yes Pages 4 Secpages 96 Order 60 Fill 49 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 90 Fullcount 225 Kwlimit 20 Idlimit 15 |
Type Secondary Compress Yes Pages 3 Secpages 5 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 5 Fullcount 5 Kwlimit 15 Idlimit 15 |
Type Secondary Compress Yes Pages 3 Secpages 1 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 1 Kwlimit 15 Idlimit 15 |
Type Secondary Compress Yes Pages 11 Secpages 331 Order 44 Fill 38 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 323 Fullcount 725 Kwlimit 32 Idlimit 15 |
Type Secondary Compress Yes Pages 3 Secpages 12 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 5 Fullcount 143 Kwlimit 15 Idlimit 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.