dbiblast.txt

emboss的linux版本的源代码

                                 dbiblast 



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.

   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.

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

   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

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: Sat 15 Jul 2006 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/06
# 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.

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     Database indexing for fasta file databases
   dbiflat      Index a flat file database
   dbigcg       Index a GCG formatted database
   dbxfasta     Database b+tree indexing for fasta file databases
   dbxflat      Database b+tree indexing for flat file databases
   dbxgcg       Database b+tree indexing for GCG formatted databases

Author(s)

   Peter Rice (pmr