pybedtools.scripts.annotate

annotate a file with the neearest features in another.

%prog [options]

if –upstream and –downstream are not specified only 2 colummns are added to the [a] file: nearest_name, nearest_distance. if they are specified upstream_names, downstream_names are specified. if –report-distance is included, the format will be:

gene:dist,gene2:dist2

for each of the up and downstream columns.

Functions

add_closest(aname, bname)

add_xstream(a, b, dist, updown[, …])

gen_get_name(b, afields)

get_gff_name(field)

main()

annotate a file with the neearest features in another.