dbxreport |
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dbxreport reads the index file, reporting on the file name, the number of index terms, the depth of the index tree, statistics of internal page types and the free space in an uncompressed index.
% dbxreport -indexdir . Validate index and report internals for dbx databases EMBOSS database name: embl Index fields [id]: id,acc Output file [embl.dbxreport]: |
Go to the output files for this example
Validate index and report internals for dbx databases 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_]+/) [-fields] string [id] A list of index fields separated by spaces or commas. (Any string) -outfile outfile [*.dbxreport] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -indexdir directory Index directory (optional) -fullreport boolean [N] Write full details to debug file 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 |
[-fields] (Parameter 2) |
string | A list of index fields separated by spaces or commas. | Any string | id |
-outfile | outfile | Output file name | Output file | <*>.dbxreport |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-indexdir | directory | Index directory (optional) | Directory | |
-fullreport | boolean | Write full details to debug file | Boolean value Yes/No | No |
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 |
Index 'id' (.xid) compressed: Yes (Compressed) cachesize: 100 (Size of cache) pagesize: 2048 (Page size) pagecount: 3 (Page count) order: 71 (Tree order) sorder: 99 (Order of secondary tree) level: 0 (Level of tree) slevel: 0 (Level of secondary tree) fill: 46 (Entries per bucket) sfill: 101 (Entries per secondary bucket) kwlimit: 15 (Max key size) count: 6 (Unique entries in index) fullcount: 6 (Total entries in index) Identifier index 'id' index found with 3 pages COUNT: 6 COUNTALL: 6 root: 1 bucket: 2 ... keys: 1 ... bkeys: 6 ... total_size: 2143 ... freespace: 5823, 94.8 of uncompressed FOUND: 6 FOUNDALL: 6 Index 'acc' (.xac) compressed: Yes (Compressed) cachesize: 100 (Size of cache) pagesize: 2048 (Page size) pagecount: 6 (Page count) order: 71 (Tree order) sorder: 99 (Order of secondary tree) level: 0 (Level of tree) slevel: 0 (Level of secondary tree) fill: 46 (Entries per bucket) sfill: 101 (Entries per secondary bucket) kwlimit: 15 (Max key size) count: 7 (Unique entries in index) fullcount: 9 (Total entries in index) Identifier index 'acc' index found with 6 pages COUNT: 7 COUNTALL: 9 root: 1 numroot: 1 bucket: 2 numbucket: 2 ... keys: 2 ... bkeys: 7 ... bdups: 1 ... bxtra: 2 ... nkeys: 3 (0) ... total_size: 2496 ... freespace: 11764, 95.7 of uncompressed FOUND: 7 FOUNDALL: 9 |
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 |
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.