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dbxflat |
% dbxflat
Index a flat file database using b+tree indices
Basename for index files: embl
Resource name: emblresource
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
REFSEQ : Refseq
Entry format [SWISS]: embl
Wildcard database filename [*.dat]: rod.dat
Database directory [.]: embl
id : ID
acc : Accession number
sv : Sequence Version and GI
des : Description
key : Keywords
org : Taxonomy
Index fields [id,acc]:
General log output file [outfile.dbxflat]:
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Go to the output files for this example
Standard (Mandatory) qualifiers:
[-dbname] string Basename for index files (Any string from 2
to 19 characters, matching regular
expression /[A-z][A-z0-9_]+/)
[-dbresource] string Resource name (Any string from 2 to 19
characters, matching regular expression
/[A-z][A-z0-9_]+/)
-idformat menu [SWISS] Entry format (Values: EMBL (EMBL);
SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); GB
(Genbank, DDBJ); REFSEQ (Refseq))
-filenames string [*.dat] Wildcard database filename (Any
string is accepted)
-directory directory [.] Database directory
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description); key (Keywords); org
(Taxonomy))
-outfile outfile [*.dbxflat] General log output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-release string [0.0] Release number (Any string up to 9
characters)
-date string [00/00/00] Index date (Date string dd/mm/yy)
-exclude string Wildcard filename(s) to exclude (Any string
is accepted)
-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 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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-dbname] (Parameter 1) |
Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| [-dbresource] (Parameter 2) |
Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||||||||
| -idformat | Entry format |
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SWISS | ||||||||||||
| -filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||||
| -directory | Database directory | Directory | . | ||||||||||||
| -fields | Index fields |
|
id,acc | ||||||||||||
| -outfile | General log output file | Output file | <*>.dbxflat | ||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||
| (none) | |||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||
| -release | Release number | Any string up to 9 characters | 0.0 | ||||||||||||
| -date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||||||||
Processing directory: /homes/user/test/embl/ Processing file: rod.dat entries: 6 (6) time: 0.0s (0.0s) Total time: 0.0s |
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database rod.dat |
Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 8 Kwlimit 15 |
Order 71 Fill 46 Pagesize 2048 Level 0 Cachesize 100 Order2 99 Fill2 101 Count 5 Kwlimit 15 |
This file contains non-printing characters and so cannot be displayed here.
This file contains non-printing characters and so cannot be displayed here.
Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like:
DB embl [ type: N dbalias: embl (see below) format: embl method: emboss directory: /data/embl file: *.dat indexdirectory: /data/embl/indexes ]The index file 'basename' given to dbxflat must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.
SET PAGESIZE 2048 SET CACHESIZE 200The above values are recommended for most systems. The PAGESIZE is a multiple of the size of disc pages the operating system buffers. The CACHESIZE is the number of disc pages dbxflat is allowed to cache.
RES embl [ type: Index idlen: 15 acclen: 15 svlen: 20 keylen: 25 deslen: 25 orglen: 25 ]The length definitions are the maximum lengths of 'words' in the field being indexed. Longer words will be truncated to the value set.
| Program name | Description |
|---|---|
| dbiblast | Index a BLAST database |
| dbifasta | Index a fasta file database |
| dbiflat | Index a flat file database |
| dbigcg | Index a GCG formatted database |
| dbxfasta | Index a fasta file database using b+tree indices |
| dbxgcg | Index a GCG formatted database using b+tree indices |