I am trying to do thousands of multiple sequence alignments with python3 using the ClustalOmegaCommandline. For the beginning, I am testing it on one fasta file ('test.fasta') which contains several protein sequences that I want to align. Here is the code that I am using, which is also provided in ClustalOmegaCommandline help.
from Bio.Align.Applications import ClustalOmegaCommandline in_file = 'test.fasta' out_file = "aligned.fasta" clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True) clustalomega_cline()
Here is the error that I get:
FileNotFoundError: [WinError 2] The system cannot find the file specified
I have checked multiple times, everything is fine with the directory and the file is there.What can be causing the error and how can I get the code to work?