biopython pairwise2 result to a file

Question

[mbk0asis]

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!

Answer 1

[Andrzej Zielezinski]

>>> from Bio.pairwise2 import format_alignment
>>> oh = open("out.txt", "w")
>>> for a in pairwise2.align.globalxx("ACCGT", "ACG"):
...     oh.write(format_alignment(*a))

[mbk0asis]

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!

[Peter]

Not sure what you've done wrong here (which version of Python was it?), but you should open the file outside both the for loops. As it is, it will restart a new output file for each pair of sequences, overwriting the alignments from past pairs of sequences.

[mbk0asis]

It's Python 2.7.6 on Ubuntu 14.04.

Thanks!

[mbk0asis]

Oops! I saved the files as plain txt files. After I added '>seq name' at the top, it worked. Thank you, Peter!

[mbk0asis]

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

[Peter]

This is not an answer to the original question - it's a revised question, or even a new question.

[mbk0asis]

OK. I will ask again in a new post. Thanks.