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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" go\-filter\-subset.pl \- extracts a subgraph from an ontology file .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& 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 \*(Aqsub{shift\->name =~ /transcr/}\*(Aq go.obo .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset \*(L"subset\*(R" filter in the ontology file (eg a \s-1GO \s0\*(L"slim\*(R" or subset), or a user-defined filter. .PP The subset can be exported in any format, including a graphical image .SH "ARGUMENTS" .IX Header "ARGUMENTS" .IP "\-id \s-1ID\s0" 4 .IX Item "-id ID" \&\s-1ID\s0 to use as leaf node in subgraph. All ancestors of this \s-1ID\s0 are included in the exported graph (unless \-partial is set) .Sp Multiple IDs can be passed .Sp .Vb 1 \& \-id ID1 \-id ID2 \-id ID3 ....etc .Ve .IP "\-subset \s-1SUBSET_ID\s0" 4 .IX Item "-subset SUBSET_ID" Extracts a named subset from the ontology file. (only works with obo format files). For example, a specific \s-1GO\s0 slim .Sp \&\s-1ONLY\s0 terms belonging to the subset are exported \- the \-partial option is automatically set .IP "\-namespace \s-1NAMESPACE\s0" 4 .IX Item "-namespace NAMESPACE" only terms in this namespace .IP "\-filter_code \s-1SUBROUTINE\s0" 4 .IX Item "-filter_code SUBROUTINE" \&\fBadvanced option\fR .Sp A subroutine with which the GO::Model::Term object is tested for inclusion in the subgraph (all ancestors are automatically included) .Sp You should have an understanding of the go-perl object model before using this option .Sp Example: .Sp .Vb 1 \& go\-filter\-subset \-filter_code \*(Aqsub {shift\->namespace eq \*(Aqmolecular_function\*(Aq}\*(Aq go.obo .Ve .Sp (the same things can be achieved with the \-namespace option) .IP "\-partial" 4 .IX Item "-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 .Sp 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 .IP "\-use_cache" 4 .IX Item "-use_cache" If this switch is specified, then caching mode is turned on. .Sp 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 \*(L".cache\*(R" suffix. .Sp The next time you parse the file, this program will automatically check for the existence of the \*(L".cache\*(R" 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. .SS "\s-1DOCUMENTATION\s0" .IX Subsection "DOCUMENTATION"