Ontology Flags¶
These are flags specific to the Ontology portion of the pipeline using either EggNOG or InterProScan. These will be used via the command line (denoted CMD) or ini file (denoted INI).
General Flags¶
--level [multi-integer] [INI]¶
- Specify Gene Ontology levels you would like to normalize to (ex: 0, 1, 2, 3, 4)
- This should only be used as a rough idea, some of the levels can vary slightly
- A level of ‘0’ indicates all levels will be printed while a level of 2 will indicate that all levels of 2 or higher will be printed.
- Any amount of these flags can be used
- Default: 0, 1
- More information at: http://geneontology.org/page/ontology-structure
--ontology [multi-integer] [INI]¶
Specify which ontology packages you would like to use
- 0 - EggNOG (default)
- 1 - InterProScan
Both or either can be specified with multiple flags
- Ex: - - ontology 0 - - ontology 1
- This will run both EggNOG and InterProScan
InterProScan Specific Flags¶
--protein [multi-string] [INI]¶
Use this option if you would like to run InterProScan
Specify databases to run against (you must have them already installed)
- tigrfam
- sfld
- prodom
- hamap
- pfam
- smart
- cdd
- prositeprofiles
- prositepatterns
- superfamily
- prints
- panther
- gene3d
- pirsf
- coils
- mobidblite