NAME

       go-filter-subset.pl - extracts a subgraph from an ontology file

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.

   DOCUMENTATION
       <http://www.godatabase.org/dev>

perl v5.36.0                                       2023-12-18                               GO-FILTER-SUBSET(1p)