I'm actually using the ClustalOmegaCommandline package and everything is working except that the aligned sequence output is completly wrong. Indeed, when I run the programme on python3 I get an alignment such this one:
ok SingleLetterAlphabet() alignment with 2 rows and 1625 columns CEHNTAGRDCEKCLDFYNDAPWGRASPTNVHECKACNCNGFSNK...--- pro1 MGGKIAAILLFAFFTSGSRSEPDFVDGQFNKINKNRVEVKCYDD...LEP pro2
And I know that it should not be aligned like that; the above sequence should be aligned further in the frame (in other word we sould not see the AA in the display, but only "-")
Here is my code:
from Bio.Align.Applications import ClustalOmegaCommandline
in_file = "/Users/etudiant/Desktop/Horizon_project/busco/Divergence/prot_ali" out_file = "/Users/etudiant/Desktop/Horizon_project/busco/Divergence/output_alignment.fasta"
def align_v1 (Fasta):
clustal_cline=ClustalOmegaCommandline(infile=Fasta, outfile=out_file) stdout, stderr = clustal_cline() MultipleSeqAlignment = AlignIO.read(out_file, "fasta") print ("ok",MultipleSeqAlignment)
Does anybody has a solution for me?