dbifasta

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Function

Description

The resulting index-file 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

% dbifasta Index a fasta file database Database name: EMROD simple : >ID idacc : >ID ACC or >ID (ACC) gcgid : >db:ID gcgidacc : >db:ID ACC dbid : >db ID ncbi : | formats ID line format [idacc]: idacc Database directory [.]: data Wildcard database filename [*.dat]: emrod Release number [0.0]: Index date [00/00/00]: General log output file [outfile.dbifasta]:

Go to the output files for this example

Command line arguments

Index a fasta file database
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -idformat           menu       [idacc] ID line format (Values: simple
                                  (>ID); idacc (>ID ACC or >ID (ACC)); gcgid
                                  (>db:ID); gcgidacc (>db:ID ACC); dbid (>db
                                  ID); ncbi (| formats))
   -directory          directory  [.] Database directory
   -filenames          string     [*.dat] Wildcard database filename (Any
                                  string)
   -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    [*.dbifasta] 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))
   -exclude            string     Wildcard filename(s) to exclude (Any string)
   -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)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-directory" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension

   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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-dbname] (Parameter 1)	string	Database name	Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/	Required
-idformat	list	ID line format	simple (>ID) idacc (>ID ACC or >ID (ACC)) gcgid (>db:ID) gcgidacc (>db:ID ACC) dbid (>db ID) ncbi (| formats)	idacc
-directory	directory	Database directory	Directory	.
-filenames	string	Wildcard database filename	Any string	*.dat
-release	string	Release number	Any string up to 9 characters	0.0
-date	string	Index date	Date string dd/mm/yy	00/00/00
-outfile	outfile	General log output file	Output file	<*>.dbifasta
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-fields	list	Index fields	acc (acnum accession number index) sv (seqvn sequence version and gi number index) des (des description index)	acc
-exclude	string	Wildcard filename(s) to exclude	Any string
-maxindex	integer	Maximum index length	Integer 0 or more	0
-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	Any string	-T . -k 1,1
-[no]systemsort	boolean	Use system sort utility	Boolean value Yes/No	Yes
-[no]cleanup	boolean	Clean up temporary files	Boolean value Yes/No	Yes
-indexoutdir	outdir	Index file output directory	Output directory	.
Associated qualifiers
"-directory" associated directory qualifiers
-extension	string	Default file extension	Any string
"-outfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-indexoutdir" associated outdir qualifiers
-extension	string	Default file extension	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

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.dbifasta

########################################
# Program: dbifasta
# Rundate: Fri 15 Jul 2011 12:00:00
# Dbname: EMROD
# Release: 0.0
# Date: 15/07/11
# CurrentDirectory: /homes/user/test/qa/dbifasta-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbifasta-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/data/
# DirectoryPath: /homes/user/test/data/
# Filenames: emrod
# Exclude: 
# Files: 1
#   File 1: /homes/user/test/data/emrod
########################################
# Commandline: dbifasta
#    -dbname EMROD
#    -idformat idacc
#    -directory ../../data
#    -filenames emrod
########################################

filename: 'emrod'
    id: 6
   acc: 6

Index acc: maxlen 6 items 6

Total 1 files 6 entries (0 duplicates)

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

Fields Indexed

References

Warnings

Diagnostic Error Messages