|   | 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]: 
 | 
Go to the output files for this example
| 
   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 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)
   -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
                                  is accepted)
   -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 is accepted)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-dbname] (Parameter 1) | Database 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 | ||||||||||||
| -outfile | General log output file | Output file | <*>.dbifasta | ||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||
| (none) | |||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||
| -fields | Index fields | 
 | acc | ||||||||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||||||||
| -maxindex | Maximum index length | Integer 0 or more | 0 | ||||||||||||
| -sortoptions | 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 is accepted | -T . -k 1,1 | ||||||||||||
| -[no]systemsort | Use system sort utility | Boolean value Yes/No | Yes | ||||||||||||
| -[no]cleanup | Clean up temporary files | Boolean value Yes/No | Yes | ||||||||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||||||||
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| 
########################################
# Program: dbifasta
# Rundate: Tue 15 Jul 2008 12:00:00
# Dbname: EMROD
# Release: 0.0
# Date: 15/07/08
# 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)
 | 
dbifasta creates four index files. All are binary but with a simple format.
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 ]
| Program name | Description | 
|---|---|
| dbiblast | Index a BLAST database | 
| dbiflat | Index a flat file database | 
| dbigcg | Index a GCG formatted database | 
| 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 |