dbifasta

 

Function

Index a fasta 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.

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.

Usage

Here is a sample session with dbifasta


% dbifasta 
Index a fasta database
Database name: EMROD
    simple : >ID
     idacc : >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]: 

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name
   -idformat           menu       ID line format
   -directory          directory  Database directory
   -filenames          string     Wildcard database filename
   -release            string     Release number
   -date               string     Index date

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       Index fields
   -exclude            string     Wildcard filename(s) to exclude
   -maxindex           integer    Maximum index length
   -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
   -[no]systemsort     boolean    Use system sort utility
   -[no]cleanup        boolean    Clean up temporary files
   -indexoutdir        outdir     Index directory

   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-dbname]
(Parameter 1)
Database name A string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required
-idformat ID line format
simple (>ID)
idacc (>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 A string up to 9 characters 0.0
-date Index date Date string dd/mm/yy 00/00/00
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-fields Index fields
acnum (Accession number)
seqvn (Sequence Version and GI)
des (Description)
acnum
-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 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.

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.

References

None.

Warnings

None.

Diagnostic Error Messages

Exit status It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
dbiblastIndex a BLAST database
dbiflatIndex a flat file database
dbigcgIndex a GCG formatted database

Author(s)

Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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