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GT-SELECT(1) GenomeTools Manual GT-SELECT(1)

NAME

gt-select - Select certain features (specified by the used options) from given GFF3 file(s).

SYNOPSIS

gt select [option ...] [GFF3_file ...]

DESCRIPTION

-retainids [yes|no]
when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)
-seqid [string]
select feature with the given sequence ID (all comments are selected). (default: undefined)
-source [string]
select feature with the given source (the source is column 2 in regular GFF3 lines) (default: undefined)
-contain [start end]
select all features which are contained in the given range (default: undefined)
-overlap [start end]
select all features which do overlap with the given range (default: undefined)
-strand [string]
select all top-level features(i.e., features without parents) whose strand equals the given one (must be one of +-.?) (default: undefined)
-targetstrand [string]
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 +-.?) (default: undefined)
-targetbest [yes|no]
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)
-hascds [yes|no]
select all top-level features which do have a CDS child (default: no)
-maxgenelength [value]
select genes up to the given maximum length (default: undefined)
-maxgenenum [value]
select the first genes up to the given maximum number (default: undefined)
-mingenescore [value]
select genes with the given minimum score (default: undefined)
-maxgenescore [value]
select genes with the given maximum score (default: undefined)
-minaveragessp [value]
set the minimum average splice site probability (default: undefined)
-rule_files
specify Lua files to be used for selection
-rule_logic [...]
select how multiple Lua files should be combined choose from AND|OR (default: AND)
-dropped_file [filename]
save non-selected features to file (default: undefined)
-v [yes|no]
be verbose (default: no)
-o [filename]
redirect output to specified file (default: undefined)
-gzip [yes|no]
write gzip compressed output file (default: no)
-bzip2 [yes|no]
write bzip2 compressed output file (default: no)
-force [yes|no]
force writing to output file (default: no)
-help
display help and exit
-version
display version information and exit
File format for option -rule_files:
The files supplied to option -rule_files define a function for filtering by user given criteria (see example below): 
function filter(gn)
  target = "exon"
  gfi = gt.feature_node_iterator_new(gn)

curnode = gfi:next()

while not(curnode == nil) do

  if (curnode:get_type() == target) then
    return false
  end
  curnode = gfi:next()
end

  return true
end
The above function iterates over all children of gn and checks whether there is a node of type exon. If there is such a node the function returns false, indicating that the parent node gn will not be sorted out.
NOTE: The function must be named filter and must return false, indicating that the node survived the filtering process.

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
09/05/2014 GenomeTools 1.5.3