Genome Assembly as Shortest Superstring (ROSALIND LONG)

Enother interesting task!
What I do: suppose there is such superstring S. Let the first read coordinate on S be 0. In MainFunc I find all right tails for first read and calculate their coordinates on S. Using recursion, I find everething that goes after first read to the right.
Then I reverse all that rests and do the same. Then I reverse it back and get the "left tail".

Given: At most 50 DNA strings whose length does not exceed 1 kbp in FASTA format (which represent reads deriving from the same strand of a single linear chromosome).

The dataset is guaranteed to satisfy the following condition: there exists a unique way to reconstruct the entire chromosome from these reads by gluing together pairs of reads that overlap by more than half their length.

Return: A shortest superstring containing all the given strings (thus corresponding to a reconstructed chromosome).

def find_middle(len1):
 if len1 % 2 == 0:
  return len1/2 + 1
 else:
  return (len1 + 1)/2

def find_max_middle(len1, len2):
 mlen1 = find_middle(len1)
 mlen2 = find_middle(len2)
 if mlen1 > mlen2:
  return mlen1
 else:
  return mlen2

def MainFunc(find_what_reads, find_where_reads, find_what_positions, res_string):
 find_what_reads1 = []
 find_what_positions1 = []
 find_what_counter = 0
 for find_what in find_what_reads:
  find_where_counter = 0
  for find_where in find_where_reads:
   find_what_len = len(find_what)
   find_where_len = len(find_where)
   max_middle = find_max_middle(find_what_len, find_where_len)
   a = find_what_len - max_middle
   find_what_part = find_what[a:]
   coincidence = find_where.find(find_what_part, 0)
   if coincidence > 0:
    find_where_res_string_position = find_what_positions[find_what_counter] + a - coincidence
    d = find_where_len - len(res_string[find_where_res_string_position:])
    if d > 0:
     res_string = res_string + find_where[-d:]  
    find_where_reads[find_where_counter] =  ''   
    find_what_reads1.append(find_where)
    find_what_positions1.append(find_where_res_string_position)
   find_where_counter += 1
  find_what_counter += 1
 if len(find_what_reads1) > 0:
  res_string = MainFunc(find_what_reads1, find_where_reads, find_what_positions1, res_string)['res_string']
  find_where_reads = MainFunc(find_what_reads1, find_where_reads, find_what_positions1, res_string)['find_where_reads']
 res = {}
 res['res_string'] = res_string
 res['find_where_reads'] = find_where_reads
 return res

def main():
 reads = []
 f = open('16.txt', 'r')
 read = ''
 for line in f:
  if line[0] != '>':
   read = read + line
  else:
   if read != '':
    read_clean = read.replace('\n', '')
    reads.append(read_clean)
   read = ''
 read_clean = read.replace('\n', '')
 reads.append(read_clean)
 res_string = reads[0]
 n = len(res_string)
 res_string_right2left = reads[0]
 find_what_positions = [0]
 find_what_reads = [reads[0]]
 res_left2right = MainFunc(find_what_reads, reads, find_what_positions, res_string)
 string_left2right = res_left2right['res_string']
 find_where_reads_left2right = res_left2right['find_where_reads']
 find_where_reads_right2left = []
 for r in find_where_reads_left2right:
  find_where_reads_right2left.append(r[::-1])
 res_right2left = MainFunc([res_string_right2left[::-1]], find_where_reads_right2left, find_what_positions, res_string_right2left[::-1])
 string_right2left = res_right2left['res_string']
 print string_right2left[n:][::-1] + string_left2right

if __name__ == '__main__':
 main()