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.)

Usage

% dbiflat Index a flat file database Database name: EMBL 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 Release number [0.0]: Index date [00/00/00]: General log output file [outfile.dbiflat]:

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [SWISS] Entry format (Values: EMBL (EMBL);
                                  SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); GB
                                  (Genbank, DDBJ); REFSEQ (Refseq))
   -directory          directory  [.] Database directory
   -filenames          string     [*.dat] Wildcard database filename (Any
                                  string is accepted)
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -outfile            outfile    [*.dbiflat] General log output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       [acc] Index fields (Values: acc (acnum
                                  accession number index); sv (seqvn sequence
                                  version and gi number index); des (des
                                  description index); key (keyword keywords
                                  index); org (taxon taxonomy and organism
                                  index))
   -exclude            string     Wildcard filename(s) to exclude (Any string
                                  is accepted)
   -maxindex           integer    [0] Maximum index length (Integer 0 or more)
   -sortoptions        string     [-T . -k 1,1] 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)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 dying program messages

Standard (Mandatory) qualifiers		Allowed values	Default
[-dbname] (Parameter 1)	Database name	Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/	Required
-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
-release	Release number	Any string up to 9 characters	0.0
-date	Index date	Date string dd/mm/yy	00/00/00
-outfile	General log output file	Output file	<*>.dbiflat
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) qualifiers		Allowed values	Default
-fields	Index fields	acc (acnum accession number index) sv (seqvn sequence version and gi number index) des (des description index) key (keyword keywords index) org (taxon taxonomy and organism index)	acc
-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 file output 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.

File: outfile.dbiflat

########################################
# Program: dbiflat
# Rundate: Tue 15 Jul 2008 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/08
# CurrentDirectory: /homes/user/test/qa/dbiflat-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiflat-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/embl/
# DirectoryPath: /homes/user/test/embl/
# Filenames: rod.dat
# Exclude: 
# Files: 1
#   File 1: /homes/user/test/embl/rod.dat
########################################
# Commandline: dbiflat
#    -dbname EMBL
#    -idformat EMBL
#    -directory ../../embl
#    -filenames rod.dat
########################################

filename: 'rod.dat'
    id: 6
   acc: 9

Index acc: maxlen 6 items 7

Total 1 files 6 entries (0 duplicates)

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

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

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments