I am attempting to use the T Coffee Commandline in Biopython to compare two multiple sequence alignments, but I am having some problems. Currently, I have:
from Bio.Align.Applications import TCoffeeCommandline cline = TCoffeeCommandline("aln_compare", al1 = "Alignment1.clustalw_aln", al2 = "Alignment2.clustalw_aln", outfile = "aln_compare.txt") print(cline)
From the T Coffee manual the command line I am attempting to use is:
t_coffee -other_pg aln_compare -al1 b30.aln -al2 p350.aln
However, when I run it I get:
raise ValueError("Option name %s was not found." % name), ValueError: Option name al2 was not found.
Also, is there a better way to do this, other than using the command line wrapper?
I am very new to this, so any help would be greatly appreciated.