dbiblast |
Please help by correcting and extending the Wiki pages.
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.
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
Index a BLAST database Version: EMBOSS:6.6.0.0 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 |
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 | ||||||
-directory | directory | Database directory | Directory | . | ||||||
-filenames | string | Wildcard database filename | Any string | Database name | ||||||
-release | string | Release number | Any string up to 9 characters | 0.0 | ||||||
-date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||
-seqtype | list | Sequence type |
|
unknown | ||||||
-blastversion | list | Blast index version |
|
unknown | ||||||
-outfile | outfile | General log output file | Output file | <*>.dbiblast | ||||||
Additional (Optional) qualifiers | ||||||||||
(none) | ||||||||||
Advanced (Unprompted) qualifiers | ||||||||||
-fields | list | Index fields |
|
acc | ||||||
-exclude | string | Wildcard filename(s) to exclude | Any string | |||||||
-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 | ||||||
-maxindex | integer | Maximum index length | Integer 0 or more | 0 | ||||||
-[no]systemsort | boolean | Use system sort utility | Boolean value Yes/No | Yes | ||||||
-[no]cleanup | boolean | Clean up temporary files | Boolean value Yes/No | Yes | ||||||
-sourcefile | boolean | Use FASTA source file | Boolean value Yes/No | No | ||||||
-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 |
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
######################################## # Program: dbiblast # Rundate: Mon 15 Jul 2013 12:00:00 # Dbname: swnew # Release: 0.0 # Date: 15/07/13 # 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.
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 ]
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.
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.