Problems with Multiple Sequence Alignments in BioPython

Question

[beckykalinger]

First of all, I'm very new to bioinformatics. I have to use BioPython to create multiple sequence alignments for an assignment using ClustalW2.

So, I installed the ClustalW2 command line and the "opuntia.fasta" file from the BioPython tutorial and wanted to try creating an alignment out of it to practice. Here is my code:

from Bio.Align.Applications import ClustalwCommandline
cline = ClustalwCommandline("clustalw2", infile="opuntia.fasta")
cline()

But when I run this, I get an error message that says "ERROR: Cannot open input file. No alignment!"

I tried using print(cline) and copying the output from that into the ClustalW command line directly, and got the same error message. All the relevant files are saved in the same directory so I have no idea why ClustalW would have trouble finding and opening the FASTA file.

I'm running Python 3.6, BioPython 1.70, and ClustalW 2.1, all on Windows.

Any help would be greatly appreciated.

[natasha.sernova]

See these posts. They may be helpful.

Problem With Clustalw Alignment Which Was Running Fine

Error while running clustaw2 in biopython from script

Python 3.4, Biopython 1.65: Writing to file both subject and query IDs from parsed BLAST output