def main(argv):
parser = OptionParser()
(opt, args) = parser.parse_args(argv)
A = [(1, 2.5), (3.5, 15), (45, 71), (74, 93)]
B = [(1.2, 2.5), (2, 7), (2, 2), (57, 84)]
print A
print B
print Utility_extended.intersect(A, B, 0.0001)
def getSharedExonicRegions(transcripts, min_width=5):
"""
shared_exons: a list of (start,end), which are shared among all transcripts in input, might breaking up existing exons.
sorted
"""
shared_exons = transcripts[0].getExons()
for index in range(1, len(transcripts)):
current_exons = transcripts[index].getExons()
shared_exons = Utility_extended.intersect(shared_exons, current_exons,
min_width)
return shared_exons #sorted
def getSharedIntronicRegions(transcripts, min_width=5):
"""
shared_introns: a list of (start,end), which are shared among all transcripts in input, might breaking up existing introns.
sorted
"""
shared_introns = transcripts[0].getIntrons()
for index in range(1, len(transcripts)):
current_introns = transcripts[index].getIntrons()
#if len(current_introns) == 0 and len(shared_introns) == 0:
#for transcript in transcripts:
#print transcript.getAll()
shared_introns = Utility_extended.intersect(shared_introns,
current_introns, min_width)
return shared_introns #sorted