dbxobo 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 an obo ontology using b+tree indices Description dbxobo indexes an ontology in OBO format, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Related application dbxedam provides additional index fields for EDAM-specific namespaces and relations. Usage Here is a sample session with dbxobo % dbxobo Index an obo ontology using b+tree indices Basename for index files: edam Standard database name [edam]: Resource name [oboresource]: oboresource Database directory [.]: Wildcard database filename [*.obo]: EDAM.obo id : ID acc : Synonym nam : Name isa : Parent des : Description ns : Namespace Index fields [*]: * Compressed index files [Y]: General log output file [outfile.dbxobo]: Go to the output files for this example Command line arguments Index an obo ontology using b+tree indices Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-dbname] string 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 [oboresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -filenames string [*.obo] Wildcard database filename (Any string) -fields menu [*] Index fields (Values: id (ID); acc (Synonym); nam (Name); isa (Parent); des (Description); ns (Namespace)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxobo] 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 dbxobo reads and indexes OBO format ontology files Output file format dbxobo creates one summary file for the database and two files for each field indexed. Output files for usage example File: outfile.dbxobo 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 200 OK. Maximum acc term length was 47 for 'HMMER profile align ment (sequences versus HMMs)'. Field nam namlen 70 OK. Maximum nam term length was 15 for 'semanticscience'. Field isa isalen 15 OK. Maximum isa term length was 4 for '0003'. Field ns nslen 20 OK. Maximum ns term length was 10 for 'identifier'. Field des deslen 50 OK. Maximum des term length was 17 for 'conceptualisation'. File: edam.ent # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database EDAM.obo File: edam.pxac Type Identifier Compress Yes Pages 3 Secpages 0 Order 76 Fill 74 Level 0 Pagesize 16384 Cachesize 20000 Order2 816 Fill2 1364 Secpagesize 16384 Seccachesize 20000 Count 143 Fullcount 143 Kwlimit 200 Reffiles 0 File: edam.pxde Type Secondary Compress Yes Pages 21 Secpages 562 Order 64 Fill 57 Level 0 Pagesize 4096 Cachesize 20000 Order2 144 Fill2 204 Secpagesize 4096 Seccachesize 20000 Count 562 Fullcount 2167 Kwlimit 50 Idlimit 15 File: edam.pxid 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 File: edam.pxis Type Secondary Compress Yes Pages 4 Secpages 96 Order 71 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 90 Fullcount 225 Kwlimit 15 Idlimit 15 File: edam.pxnm Type Secondary Compress Yes Pages 5 Secpages 323 Order 196 Fill 179 Level 0 Pagesize 16384 Cachesize 20000 Order2 583 Fill2 818 Secpagesize 16384 Seccachesize 20000 Count 323 Fullcount 725 Kwlimit 70 Idlimit 15 File: edam.pxns Type Secondary Compress Yes Pages 3 Secpages 12 Order 60 Fill 49 Level 0 Pagesize 2048 Cachesize 20000 Order2 16 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 5 Fullcount 143 Kwlimit 20 Idlimit 15 File: edam.xac This file contains non-printing characters and so cannot be displayed here. File: edam.xde This file contains non-printing characters and so cannot be displayed here. File: edam.xid This file contains non-printing characters and so cannot be displayed here. File: edam.xis This file contains non-printing characters and so cannot be displayed here. File: edam.xnm This file contains non-printing characters and so cannot be displayed here. File: edam.xns This file contains non-printing characters and so cannot be displayed here. Data files Notes References Warnings None. Diagnostic Error Messages None. Exit status It exits with a status of 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 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 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