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dbxfasta
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Index a fasta file database using b+tree indices
Description
dbxfasta indexes a flat file database of one or more files, and builds
EMBOSS B+tree format index files.
These indexes allow access of flat files larger than 2Gb.
Usage
Here is a sample session with dbxfasta
% dbxfasta
Index a fasta file database using b+tree indices
Basename for index files: emrod
Resource name: emblresource
simple : >ID
idacc : >ID ACC or >ID (ACC)
idsv : >ID SV or >ID (SV)
gcgid : >db:ID
gcgidacc : >db:ID ACC
dbid : >db ID
ncbi : | formats
ID line format [idacc]: idacc
Database directory [.]: data
Wildcard database filename [*.fasta]: emrod
id : ID
acc : Accession number
sv : Sequence Version and GI
des : Description
Index fields [id,acc]:
Compressed index files [Y]:
General log output file [outfile.dbxfasta]:
Go to the output files for this example
Command line arguments
Index a fasta file database using b+tree indices
Version: EMBOSS:6.6.0.0
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)); idsv
(>ID SV or >ID (SV)); gcgid (>db:ID);
gcgidacc (>db:ID ACC); dbid (>db ID); ncbi
(| formats))
-directory directory [.] Database directory
-filenames string [*.fasta] Wildcard database filename (Any
string)
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description))
-[no]compressed boolean [Y] Compressed index files
-outfile outfile [*.dbxfasta] 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)
-statistics boolean [N] Report I/O statistics for each input
file
-indexoutdir outdir [.] Index file output directory
Associated qualifiers:
"-directory" associated qualifiers
-extension string Default file extension
"-indexoutdir" associated qualifiers
-extension string Default file extension
"-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 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
dbxfasta reads and indexes FASTA format sequence data files.
Output file format
dbxfasta creates one summary file for the database and two files for
each field indexed.
* dbalias.ent is the master file containing the names of the files
that have been indexed. It is an ASCII file. This file also
contains the database release and date information.
* dbalias.xid is the B+tree index file for the ID names. It is a
binary file.
* dbalias.pxid is an ASCII file containing information regarding the
structure of the ID name index.
Output files for usage example
File: outfile.dbxfasta
Processing directory: /homes/user/test/data/
Processing file: emrod
entries: 6 (6) time: 0.0/0.0s (-0.0/0.0)
Total time: 0:00.0
Entry idlen 15 OK. Maximum ID length was 6 for 'L48662'.
Field acc acclen 15 OK. Maximum acc term length was 6 for 'L48662'.
File: emrod.ent
# Number of files: 1
# Release: 0.0
# Date: 00/00/00
Single filename database
emrod
File: emrod.pxac
Type Identifier
Compress Yes
Pages 3
Secpages 0
Order 71
Fill 56
Level 0
Pagesize 2048
Cachesize 20000
Order2 22
Fill2 41
Secpagesize 512
Seccachesize 20000
Count 6
Fullcount 6
Kwlimit 15
Reffiles 0
File: emrod.pxid
Type Identifier
Compress Yes
Pages 3
Secpages 0
Order 71
Fill 56
Level 0
Pagesize 2048
Cachesize 20000
Order2 22
Fill2 41
Secpagesize 512
Seccachesize 20000
Count 6
Fullcount 6
Kwlimit 15
Reffiles 0
File: emrod.xac
This file contains non-printing characters and so cannot be displayed
here.
File: emrod.xid
This file contains non-printing characters and so cannot be displayed
here.
Data files
None.
Notes
The indexing system has been designed to allow on-the-fly updating of
indexes. This feature is, however, not implemented in the current
version. It will be made available in future releases.
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.
Fields Indexed
By default, dbxfasta will index the ID name and the accession number
(if present).
If they are present in your database, you may also specify that
dbxfasta should index the Sequence Version and GI, the words in the
description, the keywords and the organism words using the '-fields'
qualifier with the appropriate values.
Global Parameters
dbxfasta requires that two global parameters be defined in the file
emboss.defaults. These are:
SET PAGESIZE 2048
SET CACHESIZE 200
The 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.
Resources
dbxfasta will ask you for the name of a resource definition in the file
emboss.defaults. This will be something like:
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.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
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
dbxcompress Compress an uncompressed dbx index
dbxedam Index the EDAM ontology 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)
Alan Bleasby
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
Target users
This program is intended to be used by administrators responsible for
software and database installation and maintenance.
Comments
None
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