dbiblast

Function

Description

The index files of the blast database format are not useful by themselves as they do not hold the entrynames or accession numbers, but they are used as pointers to the reference and sequence information in the database.

Because there are two sequence types (nucleic acid and protein) and two index formats (blast1 from pressdb or setdb, and blast2 from formatdb) with different index file names, dbiblast will ask about the database type. If the answer is "unknown" dbiblast will test each possible set of file names until one is found.

Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like:

DB swnew [
   type: P
   format: embl
   method: blast
   directory: /data/embl
]  

Fields Indexed

Indexing the Blast database

The reason is that NCBI have not documented the new format, so we cannot extend dbiblast to read it.

If you have the original (fasta format) file you can build the previous blast database format with:

formatdb -A F

This turns off the new "ASN.1" formatting. blastall will still work.

Usage

This creates EMBOSS indices for the BLAST database 'swnew'

% dbiblast Index a BLAST database Database name: swnew Database directory [.]: data Wildcard database filename [swnew]: Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: General log output file [outfile.dbiblast]:

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_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [Database name] 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)
   -seqtype            menu       [unknown] Sequence type (Values: N
                                  (nucleic); P (protein); ? (unknown))
   -blastversion       menu       [unknown] Blast index version (Values: 1
                                  (wublast and setdb/pressdb); 2 (formatdb); 0
                                  (unknown))
   -outfile            outfile    [*.dbiblast] 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
                                  is accepted)
   -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)
   -maxindex           integer    [0] Maximum index length (Integer 0 or more)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -sourcefile         boolean    Use FASTA source file
   -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 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 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
-directory	Database directory	Directory	.
-filenames	Wildcard database filename	Any string is accepted	Database name
-release	Release number	Any string up to 9 characters	0.0
-date	Index date	Date string dd/mm/yy	00/00/00
-seqtype	Sequence type	N (nucleic) P (protein) ? (unknown)	unknown
-blastversion	Blast index version	1 (wublast and setdb/pressdb) 2 (formatdb) 0 (unknown)	unknown
-outfile	General log output file	Output file	<*>.dbiblast
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)	acc
-exclude	Wildcard filename(s) to exclude	Any string is accepted	An empty string is accepted
-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
-maxindex	Maximum index length	Integer 0 or more	0
-[no]systemsort	Use system sort utility	Boolean value Yes/No	Yes
-[no]cleanup	Clean up temporary files	Boolean value Yes/No	Yes
-sourcefile	Use FASTA source file	Boolean value Yes/No	No
-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.dbiblast

########################################
# Program: dbiblast
# Rundate: Sun 15 Jul 2007 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/07
# CurrentDirectory: /homes/user/test/qa/dbiblast-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiblast-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/data/
# DirectoryPath: /homes/user/test/data/
# Filenames: swnew
# Exclude: 
# Files: 1
#   File 1: /homes/user/test/data/swnew
########################################
# Commandline: dbiblast
#    -dbname swnew
#    -directory ../../data
########################################

filename: '/homes/user/test/data/swnew'
    id: 9
   acc: 9

Index acc: maxlen 6 items 9

Total 1 files 9 entries (0 duplicates)

dbiblast 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