1Index an obo ontology using b+tree indices
2Version: EMBOSS:6.6.0.0
3
4   Standard (Mandatory) qualifiers:
5  [-dbname]            string     Basename for index files (Any string from 2
6                                  to 19 characters, matching regular
7                                  expression /[A-z][A-z0-9_]+/)
8  [-standardname]      string     [$(dbname)] Standard database name (Any
9                                  string from 2 to 19 characters, matching
10                                  regular expression /[A-z][A-z0-9_]+/)
11  [-dbresource]        string     [oboresource] Resource name (Any string from
12                                  2 to 19 characters, matching regular
13                                  expression /[A-z][A-z0-9_]+/)
14   -directory          directory  [.] Database directory
15   -filenames          string     [*.obo] Wildcard database filename (Any
16                                  string)
17   -fields             menu       [*] Index fields (Values: id (ID); acc
18                                  (Synonym); nam (Name); isa (Parent); des
19                                  (Description); ns (Namespace))
20   -[no]compressed     boolean    [Y] Compressed index files
21   -outfile            outfile    [*.dbxobo] General log output file
22
23   Additional (Optional) qualifiers: (none)
24   Advanced (Unprompted) qualifiers:
25   -release            string     [0.0] Release number (Any string up to 9
26                                  characters)
27   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
28   -exclude            string     Wildcard filename(s) to exclude (Any string)
29   -indexoutdir        outdir     [.] Index file output directory
30
31   Associated qualifiers:
32
33   "-directory" associated qualifiers
34   -extension          string     Default file extension
35
36   "-indexoutdir" associated qualifiers
37   -extension          string     Default file extension
38
39   "-outfile" associated qualifiers
40   -odirectory         string     Output directory
41
42   General qualifiers:
43   -auto               boolean    Turn off prompts
44   -stdout             boolean    Write first file to standard output
45   -filter             boolean    Read first file from standard input, write
46                                  first file to standard output
47   -options            boolean    Prompt for standard and additional values
48   -debug              boolean    Write debug output to program.dbg
49   -verbose            boolean    Report some/full command line options
50   -help               boolean    Report command line options and exit. More
51                                  information on associated and general
52                                  qualifiers can be found with -help -verbose
53   -warning            boolean    Report warnings
54   -error              boolean    Report errors
55   -fatal              boolean    Report fatal errors
56   -die                boolean    Report dying program messages
57   -version            boolean    Report version number and exit
58
59