.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "GO-FILTER-SUBSET 1p" .TH GO-FILTER-SUBSET 1p "2021-01-09" "perl v5.32.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. 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"