dbiflat

 

Function

Index a flat file database

Description

dbiflat 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.

A flat file database is a database in one of the native formats: EMBL, Swiss-Prot or GenBank, as distributed by the EBI, NCBI, or DDBJ. (It is called a 'flat' file to distinguish it from the complex relational database formats that this data is held in before being written to files and distributed.)

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: embl
   method: emblcd
   directory: /data/embl
]  

Usage

Here is a sample session with dbiflat


% dbiflat 
Index a flat file database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]: EMBL
Database directory [.]: ../../embl
Wildcard database filename [*.dat]: rod.dat
Database name: EMBL
Release number [0.0]: 
Index date [00/00/00]: 

Go to the output files for this example

Command line arguments

   Mandatory qualifiers:
   -idformat           menu       Entry 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 Entry format
EMBL (EMBL)
SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew)
GB (Genbank, DDBJ)
REFSEQ (Refseq)
SWISS
-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)
keyword (Keywords)
taxon (Taxonomy)
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 Boolean value Yes/No Yes
-[no]cleanup Clean up temporary files Boolean value Yes/No Yes

Input file format

'flat' files (native distribution format) of a protein or nucleic sequence database.

Output file format

Output files for usage example

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: 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.

dbiflat 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 exits with a status of 0 if no problems.

Known bugs

None.

See also

Program nameDescription
dbiblastIndex a BLAST database
dbifastaIndex a fasta database
dbigcgIndex a GCG formatted database

Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Completed December 1999

Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

Comments