5.8 years ago by
Korea, Republic Of
Another problem occurred!
'local' alignment gave me 'global' alignment results.
seq.fa and primer.fa are
> seq
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
>primer
CCTCAACCTTCCAG
Modified code is
from itertools import product
from Bio import SeqIO
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
seqs1 = SeqIO.to_dict(SeqIO.parse(open('./seq.fa'),'fasta'))
seqs2 = SeqIO.to_dict(SeqIO.parse(open('./primer.fa'),'fasta'))
result = open("./result.txt","w")
for sr1, sr2 in product(seqs1,seqs2):
for a in pairwise2.align.localxx(str(seqs1[sr1].seq), str(seqs2[sr2].seq)):
result.write(format_alignment(*a))
and results are
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTC-A------A----C----C-T--T-------------C-C--A--G
Score=14
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTCA-------A----C----C-T--T-------------C-C--A--G
Score=14
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTCAA-----------C----C-T--T-------------C-C--A--G
Score=14
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTC-A------A--C------C-T--T-------------C-C--A--G
Score=14
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTCA-------A--C------C-T--T-------------C-C--A--G
Score=14
CCTCAACCTTCCAGGCTCGAGACATCCTCCCACCCCAGCCTCCCTAATAG
||||||||||||||||||||||||||||||||||||||||||||||||||
CCTCAA---------C------C-T--T-------------C-C--A--G
Score=14
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modified 5.8 years ago
•
written
5.8 years ago by
mbk0asis • 610