pybedtools.scripts.annotateΒΆ

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.

Classes

Attributes Class to map between a dict of attrs and fields[8] of a GFF Interval obj.
BedTool([fn, from_string, remote])