Gene Expression (solution) Python

#!/usr/bin/python

import bisect
import time;
starttime = time.time()

genes = []; gene_lowest = 2000000000; gene_highest = 0
reads = []; reads_filtered = 0;
cache = {}

def isect(gene_id, read):
    index_b = bisect.bisect_left(genes[gene_id], read[0])
    index_e = bisect.bisect(genes[gene_id], read[1])
    #print ("indexes are [%d, %d]" % (index_b, index_e))
    return (index_e - index_b == 1 or (index_e == index_b and index_b % 2 == 1) or (index_e - index_b > 1))

def number_of_intersections(gene_id, reads):
    n = 0
    #print (genes[gene_id])
    #print (reads[0])
    #print (reads[-1])
    #if (genes[gene_id][0] > reads[-1][-1] or genes[gene_id][-1] < reads[0][0]):
    #   #print ('no intersections at all')
    #   return 0
    for r in reads:
        if isect(gene_id, r):
            return 1
    return 0
(n, m) = map(int, input().split())
# reading genes
for i in range(n):
  l = list(map(int, input().split()))
  gene_lowest = l[0] if l[0] < gene_lowest else gene_lowest
  gene_highest = l[-1] if l[1] > gene_highest else gene_highest
  #print ('gene', i, 'has', len(l)/2, 'intervals')
  genes += [l]

for i in range(m):
  l = list(map(int, input().split()))
  read = []
  for j in range(len(l) // 2):
    #if (l[j*2] < gene_highest and l[j*2+1] > gene_lowest):
    read += [(l[j*2], l[j*2+1])]
    #else:
    #    reads_filtered +=1
  if (len(read)> 0):
    reads += [read]
#print ("genes\n", genes)
#print ("reads\n", reads)
#print ('reading complete in', time.time() - starttime, 'seconds')
#print ('gene range is %d .. %d, reads filtered %d' % (gene_lowest, gene_highest, reads_filtered))

g_isect = {}
for g in range(len(genes)):
    g_isect[g] = 0

for read in reads:
    startread = time.time()
    n_of_genes = 0; gene_number = -1
    for g in range(len(genes)):
        n = number_of_intersections(g, read)
        if (n > 0):
            gene_number = g
            n_of_genes += 1
        #print (read, 'has', n, 'intersections in gene #', g, genes[g])
    if (n_of_genes == 1 and gene_number >= 0):
        #print ('adding to gene', gene_number)
        g_isect[gene_number] += 1
    #if (n_of_genes > 1):
    #   print ('Multiple hits for gene ', g)
    #print ('read processing taken %1.2f seconds for %d reads' % ( time.time() - startread, len(read)))


for g in g_isect:
    print (g_isect[g])