I have a question for MuscleCommandline.
When I use a biopython to work multiple sequence alignment using MuslceCommandline, there is an error.
The error is Non-zero return code 1, message 'Invalid command line'.
My code is
from Bio.Align.Applications import MuscleCommandline muscle_exe = r"C:\Users\user1\Desktop\Bioinformatics_with_biopython\muscle5.1.win64.exe" in_file = r"C:\Users\user1\Desktop\Bioinformatics_with_biopython\Chapter_7\HBA.all.fasta" out_file = r"C:\Users\user1\Desktop\Bioinformatics_with_biopython\Chapter_7\HBA.aln" cmd_line = MuscleCommandline(muscle_exe, input=in_file, out=out_file, clw=" ") print(cmd_line) stdout, stderr = cmd_line()
I change the path of muscle5.1.win64.exe and HBA.all.fasta.
And i also change the letter \ to / or not using r before the path.
But there was same error.
At last, I have searched my error in google and biostar etc, but there were no questions of MuscleCommandline error which is same as mine.
How can i fix it?