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