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EMBOSS
dbifasta

 

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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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-dbname]
(Parameter 1)		 string Database name Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required
-idformat list ID line format
simple (>ID)
idacc (>ID ACC or >ID (ACC))
gcgid (>db:ID)
gcgidacc (>db:ID ACC)
dbid (>db ID)
ncbi (| formats)
 idacc
-directory directory Database directory Directory .
-filenames string Wildcard database filename Any string *.dat
-release string Release number Any string up to 9 characters 0.0
-date string Index date Date string dd/mm/yy 00/00/00
-outfile outfile General log output file Output file <*>.dbifasta
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-fields list Index fields
acc (acnum accession number index)
sv (seqvn sequence version and gi number index)
des (des description index)
 acc
-exclude string Wildcard filename(s) to exclude Any string  
-maxindex integer Maximum index length Integer 0 or more 0
-sortoptions string 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 -T . -k 1,1
-[no]systemsort boolean Use system sort utility Boolean value Yes/No Yes
-[no]cleanup boolean Clean up temporary files Boolean value Yes/No Yes
-indexoutdir outdir Index file output directory Output directory .
Associated qualifiers
"-directory" associated directory qualifiers
-extension string Default file extension Any string  
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
"-indexoutdir" associated outdir qualifiers
-extension string Default file extension Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 © 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