from Bio import SeqIO from Bio import Align ref_seq_1 = SeqIO.read('C:/Users/King_Arthur/Desktop/ref_seq/segment 1/ref_seq_8.fasta','fasta') seq1 = SeqIO.read('C:/Users/King_Arthur/Desktop/file/segment 1/Myfile_1 (1).fasta','fasta') aligner = Align.PairwiseAligner() aligner.mode = 'global' aligner.match_score = 1 aligner.mismatch_score = -2 aligner.gap_score = -2 alignments = aligner.score(ref_seq_1.seq , seq1.seq) print(alignments) for alignment in sorted(alignments): print(alignment)
So this is my code and as you can see in the last section i am trying to iterate over my alignment but I am getting this error
TypeError: 'float' object is not iterable
I have tried various things like using
str() but it gives some strange values and I also tried to read the source code by using the
inspect module but I can't figure out the problem.
Any help would be really appreciated.
My final objective is to find out how many matches, mismatches and gaps are present in the final alignment using biopython.
if there is any other better way to do it in python please feel free to suggest.