dbxedam 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 the EDAM ontology using b+tree indices Description dbxedam indexes the EDAM ontology in OBO format, 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. Related application dbxobo can also index the EDAM input file. dbxedam provides additional index fields for EDAM-specific namespaces and relations. Usage Here is a sample session with dbxedam % dbxedam Index the EDAM ontology using b+tree indices Basename for index files [edam]: Standard database name [edam]: Resource name [edamresource]: Database directory [.]: Wildcard database filename [EDAM*.obo]: id : ID acc : Synonym nam : Name isa : Parent des : Description ns : Namespace hasin : has_input hasout : has_output isid : is_identifier_of isfmt : is_format_of Index fields [*]: Compressed index files [Y]: General log output file [outfile.dbxedam]: Go to the output files for this example Command line arguments Index the EDAM ontology using b+tree indices Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string [edam] 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 [edamresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -filenames string [EDAM*.obo] Wildcard database filename (Any string) -fields menu [*] Index fields (Values: id (ID); acc (Synonym); nam (Name); isa (Parent); des (Description); ns (Namespace); hasin (has_input); hasout (has_output); isid (is_identifier_of); isfmt (is_format_of)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxedam] 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 dbxedam reads and indexes the EDAM ontology file in OBO format. Output file format dbxedam 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: outfile.dbxedam Processing directory: /homes/user/test/data/ Processing file: EDAM.obo entries: 144 (144) time: 0.0s (0.0s) Total time: 0.0s 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 4 Order 87 Fill 75 Pagesize 8192 Level 0 Cachesize 100 Order2 406 Fill2 408 Count 153 Fullcount 153 Kwlimit 80 File: edam.pxde Type Secondary Compress Yes Pages 1556 Order 93 Fill 69 Pagesize 4096 Level 0 Cachesize 100 Order2 144 Fill2 204 Count 515 Fullcount 1611 Kwlimit 30 File: edam.pxhasin Type Secondary Compress Yes Pages 12 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 3 Fullcount 3 Kwlimit 15 File: edam.pxhasout Type Secondary Compress Yes Pages 15 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 4 Fullcount 7 Kwlimit 15 File: edam.pxid Type Identifier Compress Yes Pages 7 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 144 Fullcount 144 Kwlimit 15 File: edam.pxis Type Secondary Compress Yes Pages 229 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 75 Fullcount 230 Kwlimit 15 File: edam.pxisfmt Type Secondary Compress Yes Pages 24 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 7 Fullcount 20 Kwlimit 15 File: edam.pxisid Type Secondary Compress Yes Pages 6 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 1 Fullcount 1 Kwlimit 15 File: edam.pxnm Type Secondary Compress Yes Pages 622 Order 60 Fill 41 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 204 Fullcount 425 Kwlimit 20 File: edam.pxns Type Secondary Compress Yes Pages 21 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 71 Fill2 101 Count 6 Fullcount 144 Kwlimit 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.xhasin This file contains non-printing characters and so cannot be displayed here. File: edam.xhasout 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.xisfmt This file contains non-printing characters and so cannot be displayed here. File: edam.xisid 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 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 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 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