dbiflat

Function

Description

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
]  

Fields Indexed

Usage

% 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

   Standard (Mandatory) qualifiers:
   -idformat           menu       Entry format
   -directory          directory  Database directory
   -filenames          string     Wildcard database filename
  [-dbname]            string     Database name
   -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
   -indexdirectory     directory  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

   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
-idformat	Entry format	EMBL (EMBL) SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew) GB (Genbank, DDBJ) REFSEQ (Refseq)	SWISS
-directory	Database directory	Directory	.
-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
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) keyword (Keywords) taxon (Taxonomy)	acnum
-exclude	Wildcard filename(s) to exclude	Any string is accepted	An empty string is accepted
-indexdirectory	Index directory	Directory	.
-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

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.

• 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

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments