dbxresource Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Index a data resource catalogue using b+tree indices Description dbxresource indexes the Data Resource Catalogue, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. These indexes allow access of flat files larger than 2Gb. Usage Here is a sample session with dbxresource % dbxresource drcat Index a data resource catalogue using b+tree indices Standard database name [drcat]: drcat Resource name [drcatresource]: drcatresource Database directory [.]: Wildcard database filename [DRCAT.dat]: DRCAT.dat id : ID acc : IDother nam : Name des : Description url : Server URL cat : Category name taxid : Taxon id edat : EDAM data term efmt : EDAM format term eid : EDAM data id term etpc : EDAM topic term xref : Link qout : Query output qfmt : Query output format qin : Query input parameters qurl : Query URL rest : Rest URL soap : SOAP URL Index fields [*]: Compressed index files [Y]: General log output file [outfile.dbxresource]: Go to the output files for this example Command line arguments Index a data resource catalogue using b+tree indices Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string [drcat] 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 [drcatresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -filenames string [DRCAT.dat] Wildcard database filename (Any string) -fields menu [*] Index fields (Values: id (ID); acc (IDother); nam (Name); des (Description); url (Server URL); cat (Category name); taxid (Taxon id); edat (EDAM data term); efmt (EDAM format term); eid (EDAM data id term); etpc (EDAM topic term); xref (Link); qout (Query output); qfmt (Query output format); qin (Query input parameters); qurl (Query URL); rest (Rest URL); soap (SOAP URL)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxresource] 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 Input file format dbxresource reads and indexes the Data Resource Catalogue DRCAT.dat file. Output file format dbxresource creates one summary file for the database and two files for each field indexed. * dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information. * dbalias.xid is the B+tree index file for the ID names. It is a binary file. * dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index. Output files for usage example File: drcat.ent # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database DRCAT.dat File: drcat.pxac Type Identifier Compress Yes Pages 3 Order 64 Fill 43 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 21 Fullcount 21 Kwlimit 18 File: drcat.pxcat Type Secondary Compress Yes Pages 60 Order 37 Fill 29 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 19 Fullcount 72 Kwlimit 40 File: drcat.pxde Type Secondary Compress Yes Pages 2539 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 835 Fullcount 2001 Kwlimit 20 File: drcat.pxedat Type Secondary Compress Yes Pages 198 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 65 Fullcount 150 Kwlimit 15 File: drcat.pxefmt Type Secondary Compress Yes Pages 37 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 11 Fullcount 135 Kwlimit 15 File: drcat.pxeid Type Secondary Compress Yes Pages 328 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 108 Fullcount 197 Kwlimit 15 File: drcat.pxetpc Type Secondary Compress Yes Pages 204 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 67 Fullcount 204 Kwlimit 15 File: drcat.pxid Type Identifier Compress Yes Pages 8 Order 44 Fill 33 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 110 Fullcount 110 Kwlimit 32 File: drcat.pxnm Type Secondary Compress Yes Pages 1021 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 335 Fullcount 659 Kwlimit 20 File: drcat.pxqfmt Type Secondary Compress Yes Pages 52 Order 46 Fill 34 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 16 Fullcount 148 Kwlimit 30 File: drcat.pxqin Type Secondary Compress Yes Pages 377 Order 25 Fill 21 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 122 Fullcount 204 Kwlimit 65 File: drcat.pxqout Type Secondary Compress Yes Pages 391 Order 19 Fill 17 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 126 Fullcount 169 Kwlimit 90 File: drcat.pxqurl Type Secondary Compress Yes Pages 2252 Order 46 Fill 34 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 737 Fullcount 2118 Kwlimit 30 File: drcat.pxrest Type Secondary Compress Yes Pages 39 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 12 Fullcount 43 Kwlimit 20 File: drcat.pxrf Type Secondary Compress Yes Pages 15 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 4 Fullcount 87 Kwlimit 15 File: drcat.pxsoap Type Secondary Compress Yes Pages 57 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 18 Fullcount 23 Kwlimit 15 File: drcat.pxtaxid Type Secondary Compress Yes Pages 82 Order 104 Fill 58 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 26 Fullcount 114 Kwlimit 6 File: drcat.pxurl Type Secondary Compress Yes Pages 709 Order 52 Fill 37 Pagesize 2048 Level 0 Cachesize 100 Order2 44 Fill2 54 Count 231 Fullcount 594 Kwlimit 25 File: drcat.xac This file contains non-printing characters and so cannot be displayed here. File: drcat.xcat This file contains non-printing characters and so cannot be displayed here. File: drcat.xde This file contains non-printing characters and so cannot be displayed here. File: drcat.xedat This file contains non-printing characters and so cannot be displayed here. File: drcat.xefmt This file contains non-printing characters and so cannot be displayed here. File: drcat.xeid This file contains non-printing characters and so cannot be displayed here. File: drcat.xetpc This file contains non-printing characters and so cannot be displayed here. File: drcat.xid This file contains non-printing characters and so cannot be displayed here. File: drcat.xnm This file contains non-printing characters and so cannot be displayed here. File: drcat.xqfmt This file contains non-printing characters and so cannot be displayed here. File: drcat.xqin This file contains non-printing characters and so cannot be displayed here. File: drcat.xqout This file contains non-printing characters and so cannot be displayed here. File: drcat.xqurl This file contains non-printing characters and so cannot be displayed here. File: drcat.xrest This file contains non-printing characters and so cannot be displayed here. File: drcat.xrf This file contains non-printing characters and so cannot be displayed here. File: drcat.xsoap This file contains non-printing characters and so cannot be displayed here. File: drcat.xtaxid This file contains non-printing characters and so cannot be displayed here. File: drcat.xurl This file contains non-printing characters and so cannot be displayed here. File: outfile.dbxresource Processing directory: /homes/user/test/data/ Processing file: DRCAT.dat entries: 110 (110) time: 0.0s (0.0s) Total time: 0.0s Data files None. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also 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 dbxstat Dump statistics for dbx databases dbxtax Index NCBI taxonomy using b+tree indices dbxuncompress Uncompress a compressed dbx index Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by administrators responsible for software and database installation and maintenance. Comments None