dbxcompress |
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Indexes modified by dbxuncompress and indexes prior to EMBOSS 6.4.0 are uncompressed.
dbxcompress reads all pages, calculating the free space at the end of each page, and then rewrite the pages to disk removing all free space.
The final page is always written in full. This allows index reading to assume the maximum page size in all cases without reading beyond the end of file.
Uncompressed index files are required for updating an existing index. Compressed index files provide more efficient storage and retrieval.
% dbxcompress embl -indexdir . -field des Compress an uncompressed dbx index Output file [embl.dbxcompress]: |
Go to the output files for this example
Compress an uncompressed dbx index Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string EMBOSS database name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-field] string EMBOSS database field (Any string) -outfile outfile [*.dbxcompress] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -indexdir directory Index directory (optional) Associated qualifiers: "-indexdir" 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 | EMBOSS database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required |
[-field] (Parameter 2) |
string | EMBOSS database field | Any string | |
-outfile | outfile | Output file name | Output file | <*>.dbxcompress |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-indexdir | directory | Index directory (optional) | Directory | |
Associated qualifiers | ||||
"-indexdir" associated directory 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 |
Type Secondary Compress Yes Pages 647 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 213 Fullcount 417 Kwlimit 20 |
This file contains non-printing characters and so cannot be displayed here.
Compressing index 'des' for database 'embl' Index 'des' opened, compressing Completed |
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 |
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 |
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.