SYNOPSIS
go-filter-subset.pl -id GO:0003767 go.obo
go-filter-subset.pl -id GO:0003767 -to png go.obo | xv -
go-filter-subset.pl -filter_code 'sub{shift->name =~ /transcr/}' go.obo
DESCRIPTION
Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset ``subset'' filter in the ontology file (eg a GO ``slim'' or subset), or a user-defined filter.The subset can be exported in any format, including a graphical image
ARGUMENTS
- -id ID
-
ID to use as leaf node in subgraph. All ancestors of this ID are
included in the exported graph (unless -partial is set)
Multiple IDs can be passed
-id ID1 -id ID2 -id ID3 ....etc
- -subset SUBSET_ID
-
Extracts a named subset from the ontology file. (only works with obo
format files). For example, a specific GO slim
ONLY terms belonging to the subset are exported - the -partial option is automatically set
- -namespace NAMESPACE
- only terms in this namespace
- -filter_code SUBROUTINE
-
advanced option
A subroutine with which the GO::Model::Term object is tested for inclusion in the subgraph (all ancestors are automatically included)
You should have an understanding of the go-perl object model before using this option
Example:
go-filter-subset -filter_code 'sub {shift->namespace eq 'molecular_function'}' go.obo(the same things can be achieved with the -namespace option)
- -partial
-
If this is set, then only terms that match the user query are
included. Parentage is set to the next recursive parent node in the
filter
For example, with the -subset option: if X and Y belong to the subset, and Z does not, and X is_a Z is_a Y, then the exported graph withh have X is_a Y
- -use_cache
-
If this switch is specified, then caching mode is turned on.
With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ``.cache'' suffix.
The next time you parse the file, this program will automatically check for the existence of the ``.cache'' file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt.