dbxfasta 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 fasta file database using b+tree indices Description dbxfasta indexes a flat file database of one or more 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 dbxfasta % dbxfasta Index a fasta file database using b+tree indices Basename for index files: emrod Resource name: emblresource simple : >ID idacc : >ID ACC or >ID (ACC) gcgid : >db:ID gcgidacc : >db:ID ACC dbid : >db ID ncbi : | formats ID line format [idacc]: idacc Database directory [.]: data Wildcard database filename [*.fasta]: emrod id : ID acc : Accession number sv : Sequence Version and GI des : Description Index fields [id,acc]: Compressed index files [Y]: General log output file [outfile.dbxfasta]: Go to the output files for this example Command line arguments Index a fasta file database using b+tree indices Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string Basename for index files (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) [-dbresource] string Resource name (Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/) -idformat menu [idacc] ID line format (Values: simple (>ID); idacc (>ID ACC or >ID (ACC)); gcgid (>db:ID); gcgidacc (>db:ID ACC); dbid (>db ID); ncbi (| formats)) -directory directory [.] Database directory -filenames string [*.fasta] Wildcard database filename (Any string) -fields menu [id,acc] Index fields (Values: id (ID); acc (Accession number); sv (Sequence Version and GI); des (Description)) -[no]compressed boolean [Y] Compressed index files -outfile outfile [*.dbxfasta] 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 dbxfasta reads and indexes FASTA format sequence data files. Output file format dbxfasta 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.dbxfasta Processing directory: /homes/user/test/data/ Processing file: emrod entries: 6 (6) time: 0.0s (0.0s) Total time: 0.0s File: emrod.ent # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database emrod File: emrod.pxac Type Identifier Compress Yes Pages 3 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 6 Fullcount 6 Kwlimit 15 File: emrod.pxid Type Identifier Compress Yes Pages 3 Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 6 Fullcount 6 Kwlimit 15 File: emrod.xac This file contains non-printing characters and so cannot be displayed here. File: emrod.xid This file contains non-printing characters and so cannot be displayed here. Data files None. Notes The indexing system has been designed to allow on-the-fly updating of indexes. This feature is, however, not implemented in the current version. It will be made available in future releases. Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like: DB emrod [ type: N dbalias: emrod (see below) format: fasta method: emboss directory: /data/embl/fasta file: emrod.fasta indexdirectory: /data/embl/fasta/indexes ] The index file 'basename' given to dbxfasta must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes. Fields Indexed By default, dbxfasta will index the ID name and the accession number (if present). If they are present in your database, you may also specify that dbxfasta should index the Sequence Version and GI, the words in the description, the keywords and the organism words using the '-fields' qualifier with the appropriate values. Global Parameters dbxfasta requires that two global parameters be defined in the file emboss.defaults. These are: SET PAGESIZE 2048 SET CACHESIZE 200 The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxfasta is allowed to cache. Resources dbxfasta will ask you for the name of a resource definition in the file emboss.defaults. This will be something like: RES embl [ type: Index idlen: 15 acclen: 15 svlen: 20 keylen: 25 deslen: 25 orglen: 25 ] The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set. 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 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) Alan Bleasby 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