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.\" ========================================================================
.\"
.IX Title "GO-FILTER-SUBSET 1"
.TH GO-FILTER-SUBSET 1 "2010-05-12" "perl v5.12.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.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"
<http://www.godatabase.org/dev>
