Muscle alignment in python

Question

I have a problem with printing my output from muscle aligning in python. My code is:

from Bio.Align.Applications import MuscleCommandline
from StringIO import StringIO
from Bio import AlignIO

def align_v1 (Fasta): 
    muscle_cline = MuscleCommandline(input="hiv_protease_sequences_w_wt.fasta")
    stdout, stderr = muscle_cline()
    MultipleSeqAlignment = AlignIO.read(StringIO(stdout), "fasta") 
    print MultipleSeqAlignment 

Any help?

Answer 1

It would be nice to know what error you received, but the following should solve your problem:

from Bio.Align.Applications import MuscleCommandline
from StringIO import StringIO
from Bio import AlignIO

muscle_exe = r"C:muscle3.8.31_i86win32.exe" #specify the location of your muscle exe file

input_sequences = "hiv_protease_sequences_w_wt.fasta"
output_alignment = "output_alignment.fasta"

def align_v1 (Fasta): 
    muscle_cline = MuscleCommandline(muscle_exe, input=Fasta, out=output_alignment)
    stdout, stderr = muscle_cline()
    MultipleSeqAlignment = AlignIO.read(output_alignment, "fasta") 
    print MultipleSeqAlignment

align_v1(input_sequences)

In my case I received a ValueError:

>>> AlignIO.read(StringIO(stdout), "fasta") 
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:WinPython-64bit-3.3.2.3python-3.3.2.amd64libsite-packagesBioAlignIO\__init__.py", line 427, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

This could be avoided by saving the output and reopening with AlignIO.read.

I also received a FileNotFoundError that could be avoided by specifying the location of the muscle exe file. eg:

muscle_exe = r"C:muscle3.8.31_i86win32.exe" 

The instructions for this are shown in help(MuscleCommandline), but this is not currently in the Biopython tutorial page.

Finally, I am assuming you want to run the command using different input sequences, so I modifed the function to the format “function_name(input_file).”

I used python 3.3. Hopefully the code above is for python 2.x as in your original post. For python 3.x, change "from StringIO import StringIO" to "from io import StringIO" and of course “print MultipleSeqAlignment” to “print(MultipleSeqAlignment)”.