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. This 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

   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 is accepted)
   -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
                                  is accepted)
   -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 is accepted)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-dbname]
(Parameter 1)
Database name Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required
-idformat 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 Database directory Directory .
-filenames Wildcard database filename Any string is accepted *.dat
-release Release number Any string up to 9 characters 0.0
-date Index date Date string dd/mm/yy 00/00/00
-outfile General log output file Output file <*>.dbifasta
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-fields Index fields
acc (acnum accession number index)
sv (seqvn sequence version and gi number index)
des (des description index)
acc
-exclude Wildcard filename(s) to exclude Any string is accepted An empty string is accepted
-maxindex Maximum index length Integer 0 or more 0
-sortoptions 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 is accepted -T . -k 1,1
-[no]systemsort Use system sort utility Boolean value Yes/No Yes
-[no]cleanup Clean up temporary files Boolean value Yes/No Yes
-indexoutdir Index file output directory Output directory .

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: Tue 15 Jul 2008 12:00:00
# Dbname: EMROD
# Release: 0.0
# Date: 15/07/08
# 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.

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
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

Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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