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dbxfasta |
Having created the EMBOSS indexes for this file, a database can then be defined in the file emboss.defaults as something like:
DB emrod [ type: N dbalias: emrod (see below) format: fasta method: emboss directory: /data/embl/fasta file: emrod.fasta indexdirectory: /data/embl/fasta/indexes ]The index file 'basename' given to dbxfasta must match the DB name in the definition. If not, then a 'dbalias' line must be given which specifies the basename of the indexes.
% dbxfasta
Database b+tree indexing for fasta file databases
Basename for index files: emrod
Resource name: embl
simple : >ID
idacc : >ID ACC or >ID (ACC)
gcgid : >db:ID
gcgidacc : >db:ID ACC
dbid : >db ID
ncbi : | formats
ID line format [idacc]: idacc
Database directory [.]: data
Wildcard database filename [*.dat]: emrod
Release number [0.0]:
Index date [00/00/00]:
Processing file /homes/user/test/data/emrod
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Go to the output files for this example
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 dbxfasta 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.
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 [idacc] ID line format (Values: simple
(>ID); idacc (>ID ACC or >ID (ACC)); gcgid
(>db:ID); gcgidacc (>db:ID ACC); dbid (>db
ID); ncbi (| formats))
-directory directory [.] Database directory
-filenames string [*.dat] 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)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description))
-exclude string Wildcard filename(s) to exclude (Any string
is accepted)
-indexoutdir outdir [.] Index file output directory
Associated qualifiers: (none)
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
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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 | ID line format |
|
idacc | ||||||||||||
| -directory | Database directory | Directory | . | ||||||||||||
| -filenames | Wildcard database filename | Any string is accepted | *.dat | ||||||||||||
| -release | Release number | Any string up to 9 characters | 0.0 | ||||||||||||
| -date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||
| (none) | |||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||
| -fields | Index fields |
|
id,acc | ||||||||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||||||||
# Number of files: 1 # Release: 0.0 # Date: 00/00/00 Single filename database emrod |
Order 71 Fill 47 Pagesize 2048 Level 0 Cachesize 200 Order2 82 Fill2 99 Count 5 Kwlimit 15 |
Order 71 Fill 47 Pagesize 2048 Level 0 Cachesize 200 Order2 82 Fill2 99 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.
| Program name | Description |
|---|---|
| dbiblast | Index a BLAST database |
| dbifasta | Database indexing for fasta file databases |
| dbiflat | Index a flat file database |
| dbigcg | Index a GCG formatted database |
| dbxflat | Database b+tree indexing for flat file databases |
| dbxgcg | Database b+tree indexing for GCG formatted databases |