if args.mutation_details != None:
details_out = open(args.mutation_details, "w")
else:
details_out = None
for i in range(n_reads):
per_read_mutations = 0
start = random.randint(0, len_genome - READLEN)
read = genome[start:start + READLEN].upper()
# reverse complement?
is_rc = False
if random.choice([0, 1]) == 0:
is_rc = True
read = fasta.rc(read)
# error?
was_mut = False
rc_flag = 'f'
if is_rc:
rc_flag = 'r'
seq_name = "read{0}{1}".format(i, rc_flag)
orig_read = read
for _ in range(READLEN):
if ERROR_RATE > 0:
force = False
while force or random.randint(1, int(1.0/ERROR_RATE)) == 1:
force = False
pos = random.randint(1, READLEN) - 1
def test():
is_transitive(A, A, A)
is_transitive(A, A, B)
is_transitive(A, B, A)
is_transitive(A, B, B)
is_transitive(B, A, A)
is_transitive(B, A, B)
is_transitive(B, B, A)
is_transitive(B, B, B)
print 'el-br-re'
is_transitive(el, br, re)
is_transitive(el, fasta.rc(br), re)
is_transitive(el, br, fasta.rc(re))
is_transitive(el, fasta.rc(br), fasta.rc(re))
is_transitive(fasta.rc(el), br, re)
is_transitive(fasta.rc(el), fasta.rc(br), re)
is_transitive(fasta.rc(el), br, fasta.rc(re))
is_transitive(fasta.rc(el), fasta.rc(br), fasta.rc(re))