dbifasta 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 Description dbifasta indexes a flat file database of one or more files, and builds EMBL CD-ROM format index files. The resulting index-file format is used by the software on the EMBL database CD-ROM distribution and by the Staden package in addition to EMBOSS, and appears to be the most generally used and publicly available index file format for these databases. Usage Here is a sample session with dbifasta % dbifasta Index a fasta file database Database name: EMROD 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 [*.dat]: emrod Release number [0.0]: Index date [00/00/00]: General log output file [outfile.dbifasta]: Go to the output files for this example Command line arguments Index a fasta file database Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-dbname] string Database 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 [*.dat] Wildcard database filename (Any string) -release string [0.0] Release number (Any string up to 9 characters) -date string [00/00/00] Index date (Date string dd/mm/yy) -outfile outfile [*.dbifasta] General log output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -fields menu [acc] Index fields (Values: acc (acnum accession number index); sv (seqvn sequence version and gi number index); des (des description index)) -exclude string Wildcard filename(s) to exclude (Any string) -maxindex integer [0] Maximum index length (Integer 0 or more) -sortoptions string [-T . -k 1,1] Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field (Any string) -[no]systemsort boolean [Y] Use system sort utility -[no]cleanup boolean [Y] Clean up temporary files -indexoutdir outdir [.] Index file output directory Associated qualifiers: "-directory" associated qualifiers -extension string Default file extension "-outfile" associated qualifiers -odirectory string Output directory "-indexoutdir" associated qualifiers -extension string Default file extension 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 Output file format Output files for usage example File: division.lkp This file contains non-printing characters and so cannot be displayed here. File: entrynam.idx This file contains non-printing characters and so cannot be displayed here. File: acnum.hit This file contains non-printing characters and so cannot be displayed here. File: acnum.trg This file contains non-printing characters and so cannot be displayed here. File: outfile.dbifasta ######################################## # Program: dbifasta # Rundate: Fri 15 Jul 2011 12:00:00 # Dbname: EMROD # Release: 0.0 # Date: 15/07/11 # CurrentDirectory: /homes/user/test/qa/dbifasta-ex-keep/ # IndexDirectory: ./ # IndexDirectoryPath: /homes/user/test/qa/dbifasta-ex-keep/ # Maxindex: 0 # Fields: 2 # Field 1: id # Field 2: acc # Directory: /homes/user/test/data/ # DirectoryPath: /homes/user/test/data/ # Filenames: emrod # Exclude: # Files: 1 # File 1: /homes/user/test/data/emrod ######################################## # Commandline: dbifasta # -dbname EMROD # -idformat idacc # -directory ../../data # -filenames emrod ######################################## filename: 'emrod' id: 6 acc: 6 Index acc: maxlen 6 items 6 Total 1 files 6 entries (0 duplicates) dbifasta creates four index files. All are binary but with a simple format. * division.lkp is the master index file, and has a 300 byte header containing the database name and date plus information on the record size. This header is followed by one record for each database file, giving the full file name for the data file, and optionally a second sequence file. * entryname.idx is the entry name index. It has the same 300 byte header, mainly used to store the record size which will depend on the size of the longest entryname in the database. Each entry is stored in sorted alphanumeric order so that a binary search can be used to efficiently find any record. The record also holds the file number from division.lkp and the offsets in the data and sequence files for that entry. * acnum.trg holds the accession number information. The file has the usual 300 byte header, and a sorted list of record by accession number. Each accession number record contains the first record number in acnum.hit and the total number of records in acnum.hit so that secondary (duplicated) accession numbers can be searched. * acnum.hit is a very simple file. After the usual 300 byte header, each record simply holds the record number in entryname.idx. An accession number search will use acnum.trg to find a start position and number of records to read in this file, and will then simply read the entryname.idx records for each entry in turn. Data files None. Notes The indexing method depends on each entry having a unique entry name. No allowance is made for two entries with the same name so it is not possible to index EMBL and EMBLNEW together. Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like: DB emrod [ type: N format: fasta method: emblcd directory: /data/embl/fasta ] Fields Indexed By default, dbifasta will index the ID name and the accession number (if present). If they are present in your database, you may also specify that dbifasta should index the Sequence Version and GI number and the words in the description by using the '-fields' qualifier with the appropriate values. References None. Warnings None. Diagnostic Error Messages Exit status It always exits with status 0. Known bugs None. See also Program name Description dbiblast Index a BLAST 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 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 Completed August 2000 Target users This program is intended to be used by administrators responsible for software and database installation and maintenance. Comments None