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dbxtax |
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These indexes allow access of flat files larger than 2Gb.
% dbxtax
Index NCBI taxonomy using b+tree indices
Basename for index files [taxon]:
Resource name [taxresource]:
Database directory [.]: taxonomy
id : ID
acc : Synonym
tax : Scientific name
rnk : Rank
up : Parent
gc : Genetics code
mgc : Mitochondrial genetic code
Index fields [*]:
Compressed index files [Y]:
General log output file [outfile.dbxtax]:
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Go to the output files for this example
Index NCBI taxonomy using b+tree indices
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-dbname] string [taxon] Basename for index files (Any string
from 2 to 19 characters, matching regular
expression /[A-z][A-z0-9_]+/)
[-dbresource] string [taxresource] Resource name (Any string from
2 to 19 characters, matching regular
expression /[A-z][A-z0-9_]+/)
-directory directory [.] Database directory
-fields menu [*] Index fields (Values: id (ID); acc
(Synonym); tax (Scientific name); rnk
(Rank); up (Parent); gc (Genetics code); mgc
(Mitochondrial genetic code))
-[no]compressed boolean [Y] Compressed index files
-outfile outfile [*.dbxtax] 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)
-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_]+/ | taxon | ||||||||||||||
| [-dbresource] (Parameter 2) |
string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | taxresource | ||||||||||||||
| -directory | directory | Database directory | Directory | . | ||||||||||||||
| -fields | list | Index fields |
|
* | ||||||||||||||
| -[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes | ||||||||||||||
| -outfile | outfile | General log output file | Output file | <*>.dbxtax | ||||||||||||||
| 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 | ||||||||||||||
| -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/taxonomy/ Processing file: nodes.dmp entries: 41 (41) time: 0.0s (0.0s) Total time: 0.0s Entry idlen 7 OK. Maximum ID length was 6 for '117570'. Field acc acclen 15 OK. Maximum acc term length was 5 for '40673'. Field tax taxlen 120 OK. Maximum tax term length was 23 for 'Pongo abelii x pygmaeus'. Field rnk rnklen 16 OK. Maximum rnk term length was 12 for 'superkingdom'. Field up uplen 7 OK. Maximum up term length was 6 for '131567'. Field gc gclen 2 OK. Maximum gc term length was 1 for '1'. Field mgc mgclen 2 OK. Maximum mgc term length was 1 for '1'. |
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Reference 2 filename database nodes.dmp names.dmp |
Type Identifier Compress Yes Pages 3 Secpages 0 Order 71 Fill 46 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 1 Kwlimit 15 Reffiles 1 |
Type Secondary Compress Yes Pages 3 Secpages 1 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 41 Kwlimit 2 Idlimit 7 |
Type Identifier Compress Yes Pages 3 Secpages 0 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 41 Fullcount 41 Kwlimit 7 Reffiles 1 |
Type Secondary Compress Yes Pages 3 Secpages 3 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 3 Fullcount 39 Kwlimit 2 Idlimit 7 |
Type Identifier Compress Yes Pages 14 Secpages 6 Order 14 Fill 13 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 86 Fullcount 90 Kwlimit 120 Reffiles 1 |
Type Secondary Compress Yes Pages 3 Secpages 17 Order 68 Fill 45 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 17 Fullcount 41 Kwlimit 16 Idlimit 7 |
Type Identifier Compress Yes Pages 3 Secpages 12 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 33 Fullcount 41 Kwlimit 7 Reffiles 1 |
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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 |
| 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 |
| 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.