                                  dbiblast



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Function

   Index a BLAST database

Description

   dbiblast indexes a blast database created by the NCBI indexing programs
   formatdb, pressdb or setdb, 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.

   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.

Usage

   Here is a sample session with dbiblast

   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

Index a BLAST database
Version: EMBOSS:6.5.6.0

   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)
   -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)
   -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)
   -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:

   "-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


Input file format

   Any BLAST1 or BLAST2 database index files.

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 2012 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/12
# 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

   None.

Notes

   dbiblast can't use the new style of Blast indices. You must create the
   old style of Blast indices by adding -A F to the formatdb command line.

   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

   By default, dbiblast will index the ID name and the accession number
   (if present).
   If they are present in your database, you may specify that dbiblast
   should index the Sequence Version and GI number and the words in the
   description by using the '-fields' qualifier with the appropriate
   values.

  Indexing the Blast database

   dbiblast can't use the new style of Blast indices. You must create the
   old style of Blast indices by adding -A F to the formatdb command line.

   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.

References

   None.

Warnings

Diagnostic Error Messages

   None.

Exit status

   None.

Known bugs

   dbiblast can't use the new style of Blast indices. You must create the
   old style of Blast indices by adding -A F to the formatdb command line.

See also

                    Program name                       Description
                    dbifasta      Index a fasta file database
                    dbiflat       Index a flat file database
                    dbigcg        Index a GCG formatted database
                    dbxcompress   Compress an uncompressed dbx index
                    dbxedam       Index the EDAM ontology using b+tree indices
                    dbxfasta      Index a fasta file database using b+tree indices
                    dbxflat       Index a flat file database using b+tree indices
                    dbxgcg        Index a GCG formatted database using b+tree indices
                    dbxobo        Index an obo ontology using b+tree indices
                    dbxreport     Validate index and report internals for dbx databases
                    dbxresource   Index a data resource catalogue using b+tree indices
                    dbxstat       Dump statistics for dbx databases
                    dbxtax        Index NCBI taxonomy using b+tree indices
   dbxuncompress    Uncompress a compressed dbx index

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Completed        December 1999

Target users

                    This program is intended to be used by administrators responsible for
                    software and database installation and maintenance.

Comments

                    None
