AnnotateTable.py annotates individual positions of a table file according to annotations indexed by tabix tool. It adds from 1 to 3 additional columns according to -c option.
AnnotateTable.py -i mytable -a rmsk.gtf.gz -u -c1,2,3 -n rmsk -o mytable_rmsk
Options:
-a Sorted Annotation file in GTF format
-i Annotate a file of positions [column1=region, column2=coordinate (1 based)] or a single position [region:coordinate (1 based)]
-s Strand column in annotation file [4]
-u Not use table strand info (fix it to 2)
-c Add columns separated by comma (feature:1, gene_id:2, transcript_id:3) [1,2]
-n Column name [Col]
-S Correct strand by annotation
-C Columns with base distribution [7,12] (in combination with -S)
-o Save lines to a file
-h Print the help