dbxfasta

 

Function

Database b+tree indexing for fasta file databases

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.

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.

Usage

Here is a sample session with dbxfasta 


% 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

Go to the output files for this example

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.

Command line arguments 

   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

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
simple (>ID)
idacc (>ID ACC or >ID (ACC))
gcgid (>db:ID)
gcgidacc (>db:ID ACC)
dbid (>db ID)
ncbi (| formats)
 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 (ID)
acc (Accession number)
sv (Sequence Version and GI)
des (Description)
 id,acc
-exclude Wildcard filename(s) to exclude Any string is accepted An empty string is accepted
-indexoutdir Index file output directory Output directory .

Input file format

dbxfasta reads any normal sequence USAs.

Output file format

dbxfasta creates one summary file for the database and two files for each field indexed.

Output files for usage example

File: emrod.ent

# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
emrod

File: emrod.pxac

Order     71
Fill      47
Pagesize  2048
Level     0
Cachesize 200
Order2    82
Fill2     99
Count     5
Kwlimit   15

File: emrod.pxid

Order     71
Fill      47
Pagesize  2048
Level     0
Cachesize 200
Order2    82
Fill2     99
Count     5
Kwlimit   15

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.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
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

Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None