dbxtax 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 NCBI taxonomy using b+tree indices Description dbxflat indexes NCBI taxonomy files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Usage Here is a sample session with dbxtax % dbxtax Index NCBI taxonomy using b+tree indices Basename for index files [taxon]: Resource name [taxresource]: Database directory [.]: taxonomy id : ID acc : Synonym tax : Scientific name rnk : Rank up : Parent gc : Genetics code mgc : Mitochondrial genetic code Index fields [*]: Compressed index files [Y]: General log output file [outfile.dbxtax]: Go to the output files for this example Command line arguments Index NCBI taxonomy using b+tree indices Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-dbname] string [taxon] Basename for index files (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-dbresource] string [taxresource] Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -directory directory [.] Database directory -fields menu [*] Index fields (Values: id (ID); acc (Synonym); tax (Scientific name); rnk (Rank); up (Parent); gc (Genetics code); mgc (Mitochondrial genetic code)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxtax] 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) -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 dbxtax reads and indexes the NCBI taxonomy nodes.dmp, names.dmp, division.dmp, gencode.dmp,and merged.dmp files. Output file format dbxtax 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.dbxtax Processing directory: /homes/user/test/data/taxonomy/ Processing file: nodes.dmp entries: 41 (41) time: 0.0s (0.0s) Total time: 0.0s Entry idlen 7 OK. Maximum ID length was 6 for '117570'. Field acc acclen 15 OK. Maximum acc term length was 5 for '40673'. Field tax taxlen 120 OK. Maximum tax term length was 23 for 'Pongo abelii x pygm aeus'. Field rnk rnklen 16 OK. Maximum rnk term length was 12 for 'superkingdom'. Field up uplen 7 OK. Maximum up term length was 6 for '131567'. Field gc gclen 2 OK. Maximum gc term length was 1 for '1'. Field mgc mgclen 2 OK. Maximum mgc term length was 1 for '1'. File: taxon.ent # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Reference 2 filename database nodes.dmp names.dmp File: taxon.pxac Type Identifier Compress Yes Pages 3 Secpages 0 Order 71 Fill 46 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 1 Kwlimit 15 Reffiles 1 File: taxon.pxgc Type Secondary Compress Yes Pages 3 Secpages 1 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 41 Kwlimit 2 Idlimit 7 File: taxon.pxid Type Identifier Compress Yes Pages 3 Secpages 0 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 41 Fullcount 41 Kwlimit 7 Reffiles 1 File: taxon.pxmgc Type Secondary Compress Yes Pages 3 Secpages 3 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 3 Fullcount 39 Kwlimit 2 Idlimit 7 File: taxon.pxtax Type Identifier Compress Yes Pages 14 Secpages 6 Order 14 Fill 13 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 86 Fullcount 90 Kwlimit 120 Reffiles 1 File: taxon.pxrnk Type Secondary Compress Yes Pages 3 Secpages 17 Order 68 Fill 45 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 17 Fullcount 41 Kwlimit 16 Idlimit 7 File: taxon.pxup Type Identifier Compress Yes Pages 3 Secpages 12 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 33 Fullcount 41 Kwlimit 7 Reffiles 1 File: taxon.xac This file contains non-printing characters and so cannot be displayed here. File: taxon.xgc This file contains non-printing characters and so cannot be displayed here. File: taxon.xid This file contains non-printing characters and so cannot be displayed here. File: taxon.xmgc This file contains non-printing characters and so cannot be displayed here. File: taxon.xrnk This file contains non-printing characters and so cannot be displayed here. File: taxon.xtax This file contains non-printing characters and so cannot be displayed here. File: taxon.xup 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 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 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