Hello!
would somebody tell me how to save "pairwise2" result to a file instead of being printed on screen.
>>> from Bio.pairwise2 import format_alignment
>>> for a in pairwise2.align.globalxx("ACCGT", "ACG"):
... print(format_alignment(*a))
Thank you!
>>> from Bio.pairwise2 import format_alignment
>>> oh = open("out.txt", "w")
>>> for a in pairwise2.align.globalxx("ACCGT", "ACG"):
... oh.write(format_alignment(*a))
Thank you!
I'm not sure it was your code or not, but I took a code from this site and your answer and put them together.
Here's the code:
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('/home/bio1/Desktop/seq.fa'),'fasta'))
seqs2 = SeqIO.to_dict(SeqIO.parse(open('/home/bio1/Desktop/primer2.fa'),'fasta'))
for sr1, sr2 in product(seqs1,seqs2):
oh = open("/home/bio1/Desktop/result.txt", "w")
for a in pairwise2.align.localxx(str(seqs1[sr1].seq), str(seqs2[sr2].seq)):
oh.write(format_alignment(*a))
and Result:
<generator object parse at 0x7f6249c4e-e10> ||||||||||||||||||||||||||||||||||||||||||| <generator object parse at 0x7f6249c4ed7-0> Score=40 <generator object parse at 0x7f6249c4ee1-0> ||||||||||||||||||||||||||||||||||||||||||| <generator object parse at 0x7f6249c4e-d70> Score=40 <generator object parse at 0x7f6249c4ee1-0> ||||||||||||||||||||||||||||||||||||||||||| <generator object parse at 0x7f6249c4-ed70> Score=40 <generator object parse at 0x7f6249c4ee-10> ||||||||||||||||||||||||||||||||||||||||||| <generator object parse at 0x7f6249c4-ed70> Score=40 <generator object parse at 0x7f6249c4ee10> |||||||||||||||||||||||||||||||||||||||||| <generator object parse at 0x7f6249c4ed70> Score=40
Instead of DNA sequences, something else were aligned.
Would you please look into it?
Thank you, again!
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