def transform_third_codon(start, end, intervals_with_gff):
"""transform: only return nucleotide positions in window (start, end)
that are in third codon position.
"""
intervals = []
for istart, iend, gff in intervals_with_gff:
if gff.frame == ".":
raise ValueError("need a frame for third codon positions.")
# frame = nucleotides from start to next codon
frame = int(gff.frame)
# to make life easier, convert to 0-based coordinates,
# with zero starting at first position in window
# re-arrange positions on negative strand
if Genomics.IsNegativeStrand(gff.strand):
# convert to negative strand coordinates counting from 0
coordinate_offset = end
reverse = True
istart, iend = end - iend, end - istart
else:
istart, iend = istart - start, iend - start
reverse = False
coordinate_offset = start
# make sure that you start on a second codon position and within window
if istart < 0:
frame = (frame + istart) % 3
istart = 0
if frame != 0:
istart -= (3 - frame)
istart += 2
iend = min(iend, end - start)
for x in range(istart, iend, 3):
if reverse:
c = coordinate_offset - x - 1
else:
c = coordinate_offset + x
intervals.append((c, c + 1))
return Intervals.combineIntervals(intervals)
def transform_complement(start, end, intervals_with_gff):
y = Intervals.combineIntervals([(x[0], x[1]) for x in intervals_with_gff])
return Intervals.complementIntervals(y, start, end)
def transform_overlap(start, end, intervals_with_gff):
"""transform: overlap of intervals in x with y."""
y = Intervals.combineIntervals([(x[0], x[1]) for x in intervals_with_gff])
return Intervals.pruneIntervals(y, start, end)
