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 ...]

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>.