That would be a a very simple tool: feature.coord - (gene.min - 1) gives you feature.coords relative to gene.min position.

Replace the landmark column with the gene id and you get a valid gff entry again.

First, create a set of mappable genes (e.g., assuming human):

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3=="gene"' - \
    | grep -f genes.txt - \
    | convert2bed -i gff - \
    > genes.bed

Then map your GFF file (my_annotations.gff) to these genes:

$ bedmap --echo --echo-map --delim '\t' <(convert2bed -i gff < my_annotations.gff) genes.bed > answer.bed

The answer will contain your GFF annotation, and all genes (and their coordinates) which overlap your annotation by one or more bases.