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.

Usage

Here is a sample session with dbifasta, using the data in the test/wormpep directory of the distribution which is normally indexed as "wormpep"

% dbifasta
Index a fasta database
    simple : >ID
     idacc : >ID ACC
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      ncbi : >blah|...[|ACC]|ID
ID line format [idacc]: idacc
Database name: wormpep
Database directory [.]: /data/worm/
Wildcard database filename [*.dat]: wormpep 
Release number [0.0]: 1.0
Index date [00/00/00]: 04/02/00

Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers:
   -fields             menu       Index fields
   -exclude            string     wildcard filename(s) to exclude
   -indexdirectory     string     Index directory
   -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

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
-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 Any string is accepted .
-filenames Wildcard database filename Any string is accepted *.dat
[-dbname]
(Parameter 1)
Database name A string from 1 to 19 characters Required
-release Release number A string up to 9 characters 0.0
-date Index date Date string dd/mm/yy 00/00/00
Optional qualifiers Allowed values Default
(none)
Advanced 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
-indexdirectory Index directory Any 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 Yes/No Yes
-[no]cleanup Clean up temporary files Yes/No Yes

Input file format

None.

Output file format

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

None.

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)

This application was written by Alan Bleasby (ableasby@hgmp.mrc..ac.uk) Bioinformatics Division, MRC HGMP-RC, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Completed August 2000

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

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