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 filter rule files to be used for selection (terminate list with --)

       -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"
             for curnode in gn:children() do
               if (curnode:get_type() == target) then
                 return false
               end
             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>.