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dbifasta |
Wiki
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Function
Index a fasta file databaseDescription
dbifasta indexes a flat file database of one or more files, and builds EMBL CD-ROM format index files.The resulting index-file format is used by the software on the EMBL database CD-ROM distribution and by the Staden package in addition to EMBOSS, and appears to be the most generally used and publicly available index file format for these databases.
Usage
Here is a sample session with dbifasta
% dbifasta
Index a fasta file database
Database name: EMROD
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]:
General log output file [outfile.dbifasta]:
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Go to the output files for this example
Command line arguments
Index a fasta file 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_]+/)
-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)
-release string [0.0] Release number (Any string up to 9
characters)
-date string [00/00/00] Index date (Date string dd/mm/yy)
-outfile outfile [*.dbifasta] 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)
-maxindex integer [0] Maximum index length (Integer 0 or more)
-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)
-[no]systemsort boolean [Y] Use system sort utility
-[no]cleanup boolean [Y] Clean up temporary files
-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
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| 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 | ||||||||||||
| -idformat | list | ID line format |
|
idacc | ||||||||||||
| -directory | directory | Database directory | Directory | . | ||||||||||||
| -filenames | string | Wildcard database filename | Any string | *.dat | ||||||||||||
| -release | string | Release number | Any string up to 9 characters | 0.0 | ||||||||||||
| -date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||
| -outfile | outfile | General log output file | Output file | <*>.dbifasta | ||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||
| (none) | ||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||
| -fields | list | Index fields |
|
acc | ||||||||||||
| -exclude | string | Wildcard filename(s) to exclude | Any string | |||||||||||||
| -maxindex | integer | Maximum index length | Integer 0 or more | 0 | ||||||||||||
| -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 | ||||||||||||
| -[no]systemsort | boolean | Use system sort utility | Boolean value Yes/No | Yes | ||||||||||||
| -[no]cleanup | boolean | Clean up temporary files | Boolean value Yes/No | Yes | ||||||||||||
| -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 | ||||||||||||
Input file format
Output file format
Output files for usage example
File: division.lkp
This file contains non-printing characters and so cannot be displayed here.
File: entrynam.idx
This file contains non-printing characters and so cannot be displayed here.
File: acnum.hit
This file contains non-printing characters and so cannot be displayed here.
File: acnum.trg
This file contains non-printing characters and so cannot be displayed here.
File: outfile.dbifasta
########################################
# Program: dbifasta
# Rundate: Mon 15 Jul 2013 12:00:00
# Dbname: EMROD
# Release: 0.0
# Date: 15/07/13
# CurrentDirectory: /homes/user/test/qa/dbifasta-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbifasta-ex-keep/
# Maxindex: 0
# Fields: 2
# Field 1: id
# Field 2: acc
# Directory: /homes/user/test/data/
# DirectoryPath: /homes/user/test/data/
# Filenames: emrod
# Exclude:
# Files: 1
# File 1: /homes/user/test/data/emrod
########################################
# Commandline: dbifasta
# -dbname EMROD
# -idformat idacc
# -directory ../../data
# -filenames emrod
########################################
filename: 'emrod'
id: 6
acc: 6
Index acc: maxlen 6 items 6
Total 1 files 6 entries (0 duplicates)
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dbifasta creates four index files. All are binary but with a simple format.
- division.lkp is the master index file, and has a 300 byte header containing the database name and date plus information on the record size. This header is followed by one record for each database file, giving the full file name for the data file, and optionally a second sequence file.
- entryname.idx is the entry name index. It has the same 300 byte header, mainly used to store the record size which will depend on the size of the longest entryname in the database. Each entry is stored in sorted alphanumeric order so that a binary search can be used to efficiently find any record. The record also holds the file number from division.lkp and the offsets in the data and sequence files for that entry.
- acnum.trg holds the accession number information. The file has the usual 300 byte header, and a sorted list of record by accession number. Each accession number record contains the first record number in acnum.hit and the total number of records in acnum.hit so that secondary (duplicated) accession numbers can be searched.
- acnum.hit is a very simple file. After the usual 300 byte header, each record simply holds the record number in entryname.idx. An accession number search will use acnum.trg to find a start position and number of records to read in this file, and will then simply read the entryname.idx records for each entry in turn.
Data files
None.Notes
The indexing method depends on each entry having a unique entry name. No allowance is made for two entries with the same name so it is not possible to index EMBL and EMBLNEW together.Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like:
DB emrod [ type: N format: fasta method: emblcd directory: /data/embl/fasta ]
Fields Indexed
By default, dbifasta will index the ID name and the accession number (if present).If they are present in your database, you may also specify that dbifasta should index the Sequence Version and GI number and the words in the description by using the '-fields' qualifier with the appropriate values.
References
None.Warnings
None.Diagnostic Error Messages
Known bugs
None.See also
| Program name | Description |
|---|---|
| dbiblast | Index a BLAST 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 |
Author(s)
Alan BleasbyEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.