I want to use a specific blosum matrix for doing multiple sequence alignment using biopython. There are several options for doing MSA in biopython, for example I used clustalw. However, if I want to use its pwmatrix option to specify a blosum matrix, there is no kwarg for doing so. There is only an option to specify a path to matrix file, which when I specify the path of blosum62.cmp file, it gives me an error, saying 'WARNING: residue i in matrix blosum62.cmp not recognised'. I don't know how to specify a particular blosum matrix for alignment. My goal is to do my alignment using a specifc user-defined substitution matrix, therefore if anyone knows another python module to do so, I'll appreciate if you could mention its name. My Code:
from Bio.Align.Applications import ClustalwCommandline
cline = ClustalwCommandline('clustalw', infile = 'opuntia.fasta')
cline.pwmatrix = 'blosum62.cmp'
cline()
output:
ApplicationError Traceback (most recent call last)
<ipython-input-30-c418dc64da4a> in <module>
----> 1 cline()
~/anaconda3/lib/python3.7/site-packages/Bio/Application/__init__.py in __call__(self, stdin, stdout, stderr, cwd, env)
526 if return_code:
527 raise ApplicationError(return_code, str(self),
--> 528 stdout_str, stderr_str)
529 return stdout_str, stderr_str
530
ApplicationError: Non-zero return code 1 from 'clustalw -infile=opuntia.fasta -pwmatrix=blosum62.cmp', message
'WARNING: residue i in matrix blosum62.cmp not recognised'
