Closed jjtapia closed 2 years ago
Consider the following sequences
>dummy AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >ref_dummy AAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
With a one nucleotide difference. Running
./ssw_test target.fasta ref.fasta -c -s -h
will return a result with a cigar code of
26=1X33=
Which I believe is the correct one. Using ssw-py consider now the equivalent python code of
seq = 'A' * 60 ref_seq = 'A' * 24 + 'AAT' + 'A' * 33 from ssw import SSW tester = SSW() tester.setRead(seq) tester.setReference(ref_seq) res = tester.align() print(res.CIGAR)
This returns a cigar code of
60M
The same will happen if you run the default python code in the repo
res = ssw_main({'bPath':True, 'bSam':True, 'query':seq, 'targetseq':ref_seq, 'sRId': 'ref', 'bHeader':True, 'targetname':'dummy_ref'}) print(res.getvalue())
Will return a cigar value of 60M, which totally misses the mismatch.
Consider the following sequences
With a one nucleotide difference. Running
./ssw_test target.fasta ref.fasta -c -s -hwill return a result with a cigar code of
Which I believe is the correct one. Using ssw-py consider now the equivalent python code of
This returns a cigar code of
The same will happen if you run the default python code in the repo
Will return a cigar value of 60M, which totally misses the mismatch.