I'm trying to align some palindrome sequences, and there is a weird behavior of cigar string.
import parasail
def test():
a = 'AAAAGACTTGGCTCGACAACGC'
b = 'GCGTTGTCGAGCCAAGTCTTTT' # reverse complement of a
c = a + b[0:10]
m = parasail.matrix_create("ACGT", 3, -4)
r = parasail.sw_trace_striped_8(b, c, 4, 4, m)
print(r.cigar.beg_ref, r.end_ref)
print(r.cigar.beg_query, r.end_query)
print(r.cigar.decode)
# output
# 0 31
# 0 9
# b'22D10='
Cigar string starts with a 22D. The begin and end positions are wrong as well, should be (22,32) in ref and (0,10) in query since there is 10= in cigar.
I'm trying to align some palindrome sequences, and there is a weird behavior of cigar string.
Cigar string starts with a
22D
. The begin and end positions are wrong as well, should be (22,32) in ref and (0,10) in query since there is10=
in cigar.