Question: Trying to run clustalw with biopython on jupyter notebook
0
gravatar for psschlogl
25 days ago by
psschlogl0
psschlogl0 wrote:

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

biopython custalw • 111 views
ADD COMMENTlink modified 25 days ago • written 25 days ago by psschlogl0

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

ADD REPLYlink modified 25 days ago • written 25 days ago by genomax68k

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()
ADD REPLYlink modified 25 days ago • written 25 days ago by psschlogl0

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

ADD REPLYlink modified 25 days ago • written 25 days ago by genomax68k
1
gravatar for psschlogl
25 days ago by
psschlogl0
psschlogl0 wrote:

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

ADD COMMENTlink modified 24 days ago • written 25 days ago by psschlogl0
1

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

ADD REPLYlink written 25 days ago by RamRS21k
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