EMBOSS: dbiflat

Program 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.

Usage

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


% dbiflat
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
Entry format [SWISS]: EMBL
Database name: tembl
Database directory [.]: /nfs/disk42/pmr/emboss/osf/emboss/test/embl/
Wildcard database filename [*.dat]: 
Release number [0.0]: 1.0
Index date [00/00/00]: 04/02/00

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     bool       Use system sort utility
   -[no]cleanup        bool       Clean up temporary files

   General qualifiers:
  -help                bool       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)
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 Yes/No Yes

-[no]cleanup Clean up temporary files Yes/No Yes

Input file format

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

Output file format

dbiflat 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.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0 if no problems.

Known bugs

None.

Program name	Description
dbiblast	Index a BLAST database
dbifasta	Index a fasta database
dbigcg	Index 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.

EMBOSS: dbiflat

Program dbiflat

Function

Description

Usage

Command line arguments

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments