Shore annotate region

shore annotate_region can be used to annotate previously defined genomic regions with the overlapping or nearest genes present in an annotation file. Only the central base of each region will be annotated. The annotation file must be in standard GFF format.

Usage: shore annotate_region [OPTIONS]

Mandatory
-a, --annotation-file=<arg>		Annotation file
-f, --feature-file=<arg>		File with the features to be annotated. This file must contain a header specifying the columns 'chr', 'pos' and optionally 'size' or 'end'
-o, --outfile=<arg>	(Default: stdout)	Output file
Optional
--header=<arg[,...]>		Header for the feature file
--range		Use the real regions and not just the central base
--gff		Write output in GFF format
--so-filter=<arg[,...]>	(Default: gene,transposable_element_gene)	Only parse toplevel features of the given Sequence Ontology (SO) types
--print		Just print the annotation tree
--query-pos=<arg>		Query annotation for the given position