Trying to run clustalw with biopython on jupyter notebook

Question

[psschlogl]

I am trying to run a tutorial on notebooks and I am receiving this error:

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw = "bin/clustalw"
clustalw_cline = ClustalwCommandline(clustalw, infile="data/opuntia.fasta")
assert os.path.isfile(clustalw), "ClustalW executable missing"
stdout, stderr = clustalw_cline()

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-115-5a9268f91219> in <module>
      3 clustalw = "bin/./clustalw"
      4 clustalw_cline = ClustalwCommandline(clustalw, infile="data/opuntia.fasta")
----> 5 assert os.path.isfile(clustalw), "ClustalW executable missing"
      6 stdout, stderr = clustalw_cline()

AssertionError: ClustalW executable missing

But I installed my clustalw with sudo apt-get and it is in usr/bin/clustalw and i can run the program on most of the places in my cli shell, but not in te notebook.

Any of the guys here have some solution?
CLUSTAL 2.1
ubuntu debian 16.04
Biopython 1.73

Thanks

Paulo

I edited my question.
Sorry

[GenoMax]

Why are you using windows style file paths (and a windows executable clustalw2.exe), if all this is happening on Ubuntu?

[psschlogl]

I change it to ubuntu. tried :
~/usr/bin/clustalw
usr/bin/clustalw
bin/clustalw
with ./clustalw and many more.

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = "clustalw2.exe"
clustalw_cline = ClustalwCommandline("~/usr/bin/clustalw, infile=data/opuntia.fasta")
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
stdout, stderr = clustalw_cline()

[GenoMax]

What does that mean? You will need to use unix file paths and proper executable if you are actually using Ubuntu.

Answer 1

[psschlogl]

I got it done. I simple didint need all that code

from Bio.Align.Applications import ClustalwCommandline
cline = ClustalwCommandline("clustalw2", infile="seqs.fasta")
from Bio import AlignIO
align = AlignIO.read("data/opuntia.aln", "clustal")
print(align)

And that works great. Thank you

[Ram]

Please edit your answer and add how you got it working - this would help others facing similar problems in the future.

Answer 2

[874681817]

I just solved this problem. First ，you have to make sure that you have clustalw2 installed on your computer. Next，add clustalw2 paths to environment variables Last，run the following code：

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = r"C:\Program Files (x86)\ClustalW2\clustalw2.exe"   #Please fill in the software location correctly.
clustalw_cline = ClustalwCommandline(clustalw_exe, infile="opuntia.fasta")
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
stdout, stderr = clustalw_cline()

Goodluck！