bx.align.tools.tile module

Tools for tiling / projecting alignments onto an interval of a sequence.

bx.align.tools.tile.intervals_from_mask(mask)

bx.align.tools.tile.tile_interval(sources, index, ref_src, start, end, seq_db=None)

Tile maf blocks onto an interval. The resulting block will span the interval exactly and contain the column from the highest scoring alignment at each position.

sources: list of sequence source names to include in final block index: an instnace that can return maf blocks overlapping intervals ref_src: source name of the interval (ie, hg17.chr7) start: start of interval end: end of interval seq_db: a mapping for source names in the reference species to nib files