Clustalw Alignment Error In Biopython

Question

[Mkl]

Hi ,

I tried the following code to run clustalw . But I am getting error.

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

IOError: [Errno 2] No such file or directory: 'seqs.aln'

I am using winndows OS, Biopython 1.57.

I modified the previous code as shown below

>>> from Bio.Align.Applications import ClustalwCommandline
>>> clustalw_exe = r"C:\Program Files\clustalw2\clustalw2.exe"
>>> clustalw_cline = ClustalwCommandline(clustalw_exe, infile="C:\Users\ss          \Desktop\seqs.fasta")
>>> assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
>>> stdout, stderr = clustalw_cline()
>>> from Bio import AlignIO
>>> align = AlignIO.read("seqs.aln", "clustal")

But I got the error like this

  File "<pyshell#53>", line 1, in <module>
    align = AlignIO.read("seqs.aln", "clustal")
File "C:\Python27\lib\site-packages\Bio\AlignIO\__init__.py", line 427, in read
first = iterator.next()
File "C:\Python27\lib\site-packages\Bio\AlignIO\__init__.py", line 333, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'seqs.aln'

How to solve this error? Any suggestions please.

[Brad Chapman]

Your code does not actually run clustalw; you've only printed out the commandline. Try "cline()" and check out the Tutorial for more details: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc75

[Michael]

No such file or directory: 'seqs.aln'!!!

[Harpalss]

Strange I'm getting the same problem too. I'm also on windows and it does not make the alignment file or the dnd file.

[Niek De Klein]

you have spaces in your path here: s"C:Usersss Desktopseqs.fasta", does your folder also have those spaces? And is seqs.aln in the same folder clustalw2.exe?

[Mkl]

When I gave the path for seqs.aln file I got the output.

Answer 1

[Kashyap Chhatbar]

Dear MKL,

The code you have tried there is almost correct. Just a Brad Chapman mentioned that you have to try this

cline()

instead of

print cline

cline() executes ClustaW with the given parameters. I'm using Linux and I was successful using this code

from Bio.Align.Applications import ClustalwCommandline

#clustalw instead of clustalw2
cline = ClustalwCommandline("clustalw", infile="seq.fasta")
cline()

from Bio import AlignIO
align = AlignIO.read("seq.aln", "clustal")

[Mkl]

Thank you for your answer.I tried cline() instead of print cline().But I am getting error.

[Kashyap Chhatbar]

I suppose there is some misconfiguration of Biopython with your Python... Have you tried reinstalling Python and Biopython? Use the latest version of Python 2.7 from this page:http://python.org/download/ and Biopython for Python 2.7 from this page: http://biopython.org/wiki/Download.. I am pretty sure it should work.

Answer 2

[Thaman]

I have already clearly answered; please try to search specific tag >>> A: How To Run Clustalw Using Commands From An Input File