'\" t
.\"     Title: gt-select
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-SELECT" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-select \- Select certain features (specified by the used options) from given GFF3 file(s)\&.
.SH "SYNOPSIS"
.sp
\fBgt select\fR [option \&...] [GFF3_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-retainids\fR [\fIyes|no\fR]
.RS 4
when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)
.RE
.PP
\fB\-seqid\fR [\fIstring\fR]
.RS 4
select feature with the given sequence ID (all comments are selected)\&. (default: undefined)
.RE
.PP
\fB\-source\fR [\fIstring\fR]
.RS 4
select feature with the given source (the source is column 2 in regular GFF3 lines) (default: undefined)
.RE
.PP
\fB\-contain\fR [\fIstart\fR \fIend\fR]
.RS 4
select all features which are contained in the given range (default: undefined)
.RE
.PP
\fB\-overlap\fR [\fIstart\fR \fIend\fR]
.RS 4
select all features which do overlap with the given range (default: undefined)
.RE
.PP
\fB\-strand\fR [\fIstring\fR]
.RS 4
select all top\-level features(i\&.e\&., features without parents) whose strand equals the given one (must be one of
\fI+\-\&.?\fR) (default: undefined)
.RE
.PP
\fB\-targetstrand\fR [\fIstring\fR]
.RS 4
select all top\-level features (i\&.e\&., features without parents) which have exactly one target attribute whose strand equals the given one (must be one of
\fI+\-\&.?\fR) (default: undefined)
.RE
.PP
\fB\-targetbest\fR [\fIyes|no\fR]
.RS 4
if multiple top\-level features (i\&.e\&., features without parents) with exactly one target attribute have the same target_id, keep only the feature with the best score\&. If \-targetstrand is used at the same time, this option is applied after \-targetstrand\&. Memory consumption is proportional to the input file size(s)\&. (default: no)
.RE
.PP
\fB\-hascds\fR [\fIyes|no\fR]
.RS 4
select all top\-level features which do have a CDS child (default: no)
.RE
.PP
\fB\-maxgenelength\fR [\fIvalue\fR]
.RS 4
select genes up to the given maximum length (default: undefined)
.RE
.PP
\fB\-maxgenenum\fR [\fIvalue\fR]
.RS 4
select the first genes up to the given maximum number (default: undefined)
.RE
.PP
\fB\-mingenescore\fR [\fIvalue\fR]
.RS 4
select genes with the given minimum score (default: undefined)
.RE
.PP
\fB\-maxgenescore\fR [\fIvalue\fR]
.RS 4
select genes with the given maximum score (default: undefined)
.RE
.PP
\fB\-minaveragessp\fR [\fIvalue\fR]
.RS 4
set the minimum average splice site probability (default: undefined)
.RE
.PP
\fB\-rule_files\fR
.RS 4
specify Lua filter rule files to be used for selection (terminate list with
\fI\-\-\fR)
.RE
.PP
\fB\-rule_logic\fR [\fI\&...\fR]
.RS 4
select how multiple Lua files should be combined choose from AND|OR (default: AND)
.RE
.PP
\fB\-dropped_file\fR [\fIfilename\fR]
.RS 4
save non\-selected features to file (default: undefined)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
File format for option \fI\-rule_files\fR:
.sp
The files supplied to option \fI\-rule_files\fR define a function for filtering by user given criteria (see example below):
.sp
.if n \{\
.RS 4
.\}
.nf
function filter(gn)
  target = "exon"
  for curnode in gn:children() do
    if (curnode:get_type() == target) then
      return false
    end
  end
  return true
end
.fi
.if n \{\
.RE
.\}
.sp
The above function iterates over all children of \fIgn\fR and checks whether there is a node of type \fIexon\fR\&. If there is such a node the function returns \fIfalse\fR, indicating that the parent node \fIgn\fR will not be sorted out\&.
.sp
NOTE: The function must be named \fIfilter\fR and must return \fIfalse\fR, indicating that the node survived the filtering process\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.