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) |
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add_xstream (a, b, dist, updown[, ...]) |
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gen_get_name (b, afields) |
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get_gff_name (field) |
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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]) |