NAME

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

SYNOPSIS

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

OPTIONS

       -seqid
           select feature with the given sequence ID (all comments are selected). (default:
           undefined)

       -source
           select feature with the given source (the source is column 2 in regular GFF3 lines)
           (default: undefined)

       -contain
           select all features which are contained in the given range (default: undefined)

       -overlap
           select all features which do overlap with the given range (default: undefined)

       -strand
           select all top-level features(i.e., features without parents) whose strand equals the
           given one (must be one of +-.?) (default: undefined)

       -targetstrand
           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
           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
           select all top-level features which do have a CDS child (default: no)

       -maxgenelength
           select genes up to the given maximum length (default: undefined)

       -maxgenenum
           select the first genes up to the given maximum number (default: undefined)

       -mingenescore
           select genes with the given minimum score (default: undefined)

       -maxgenescore
           select genes with the given maximum score (default: undefined)

       -minaveragessp
           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
           save non-selected features to file (default: undefined)

       -v
           be verbose (default: no)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

DESCRIPTION

       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.

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                            10/07/2012                               GT-SELECT(1)