Biopython problem again

Question

[psschlogl]

I am trying to use this tutorial and I got a problem with it:

from Bio import pairwise2
from Bio import SeqIO
from Bio.pairwise2 import format_alignment

seq1 = SeqIO.read("data/alpha.faa", "fasta")
seq2 = SeqIO.read("data/beta.faa", "fasta")
alignments = pairwise2.align.globalxx(seq1.seq, seq2.seq)
print(pairwise2.format_alignment(*alignment[0]))

But I am got this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-144-da7cdbf0f1b6> in <module>
      1 from Bio.pairwise2 import format_alignment
      2 
----> 3 print(pairwise2.format_alignment(*alignment[0]))

TypeError: format_alignment() takes 5 positional arguments but 52 were given

I am just folliwing along with the biopython tutorial. Looks like in my code the function is receiving more args than due, but it looks works with the tutorial.

Some of you had a alike issue?

Thanks

Answer 1

[AK]

Hi psschlogl,

How many sequences are there in your alpha.faa and beta.faa? If both contain one, it works for me:

$ cat data/alpha.faa
>seq1
MLLPLRRVLLKAVRQHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEML
PTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVFLELHYKGSLDSAQP
$ cat data/beta.faa
>seq2
MLLPLRRVLLQHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEMLHKR
PTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVFL

$ cat test.py
#!/usr/bin/env python

from Bio import pairwise2
from Bio import SeqIO
from Bio.pairwise2 import format_alignment

seq1 = SeqIO.read("data/alpha.faa", "fasta")
seq2 = SeqIO.read("data/beta.faa", "fasta")
alignments = pairwise2.align.globalxx(seq1.seq, seq2.seq)

print(pairwise2.format_alignment(*alignments[0]))

$ python test.py
MLLPLRRVLLKAVRQHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEML---PTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVFLELHYKGSLDSAQP
||||||||||    ||||||||||||||||||||||||||||||||||||||||||||||||||||||   ||||||||||||||||||||||||||||||||||||||||||||||||||        |
MLLPLRRVLL----QHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEMLHKRPTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVF--------L-----
  Score=115

[psschlogl]

Hey bro,

you got it done!

Thank you for your time and kindness.

Paulo

[AK]

You're welcome, good luck!