def test_properties(self):
"""Test setting options via properties."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
cline = ClustalOmegaCommandline(clustalo_exe)
cline.infile = input_file
cline.outfile = output_file
cline.outfmt = "clustal"
self.standard_test_procedure(cline)
def test_properties(self):
"""Test setting options via properties."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
cline = ClustalOmegaCommandline(clustalo_exe)
cline.infile = input_file
cline.outfile = output_file
cline.outfmt = "clustal"
self.standard_test_procedure(cline)
def global_msa(matches, search_seq, file_name="msa"):
"""
Generates a global multiple sequence alignment from a list of seqs
"""
# Build list of sequences for input FASTA file
# Start with original search + others for comparison
# NOTE: synapsin paralogs are currently hard-coded
seqs = [search_seq,
SeqIO.read("synapsinIIa.fasta", "fasta"),
SeqIO.read("synapsinIIb.fasta", "fasta"),
SeqIO.read("synapsinIII.fasta", "fasta")]
# SeqIO.read("GFPclover.fasta", "fasta")]
# SeqIO.read("FireflyLuciferase.fasta", "fasta")]
# Build Biopython Seq objects from sequences
for match in matches:
# Remove gaps from AA sequence to build Seq object's sequence
# "L*R" somehow breaks things! This is a hack-y solution
# Better might be this:
# ''.join(re.split("\w\*", match["subject"])).replace("-", "")
seq = SeqRecord(Seq(match["subject"].replace("-", "").replace("L*R", "L-R"),
IUPAC.protein),
id="gi|" + match["gi"],
description=match["title"])
seqs.append(seq)
# Make FASTA file from sequences
infile = f"{file_name}_in.fasta"
SeqIO.write(seqs, infile, "fasta")
# Set up and run ClustalOmega
clustal = ClustalOmegaCommandline()
clustal.program_name = "./clustalo"
outfile = f"{file_name}_out.aln"
clustal.outfmt = "clustal"
clustal.infile = infile
clustal.outfile = outfile
clustal.force = True # Allows overwriting file
# Run MSA, print success/failure
print(f"Performing multiple sequence alignment on {len(seqs)} sequences")
stdout, stderr = clustal()
print(stdout + stderr)
print(f"Results saved as '{outfile}' to {os.getcwd()}\n")
# Return MSA file name
return outfile
