def identify_lasso_motifs(
leader: str, core: str) -> Tuple[List[int], int, Dict[int, float]]:
"""Run FIMO to identify lasso peptide-specific motifs"""
motif_file = path.get_full_path(__file__, 'data', "lasso_motifs_meme.txt")
with TemporaryFile() as tempfile:
out_file = open(tempfile.name, "w")
out_file.write(">query\n%s%s" % (leader, core))
out_file.close()
fimo_output = subprocessing.run_fimo_simple(motif_file, tempfile.name)
fimo_motifs = [
int(line.partition("\t")[0]) for line in fimo_output.split("\n")
if "\t" in line and line.partition("\t")[0].isdigit()
]
fimo_scores = {
int(line.split("\t")[0]): float(line.split("\t")[5])
for line in fimo_output.split("\n")
if "\t" in line and line.partition("\t")[0].isdigit()
}
# Calculate score
motif_score = 0
if 2 in fimo_motifs:
motif_score += 4
elif fimo_motifs:
motif_score += 2
else:
motif_score += -1
return fimo_motifs, motif_score, fimo_scores
def identify_lanthi_motifs(leader: str, core: str) -> Dict[int, float]:
"""Run FIMO to identify lanthipeptide-specific motifs"""
motifs_file = path.get_full_path(__file__, "data", "lanthi_motifs_meme.txt")
with NamedTemporaryFile() as tempfile:
out_file = open(tempfile.name, "w")
out_file.write(">query\n%s%s" % (leader, core))
out_file.close()
fimo_output = subprocessing.run_fimo_simple(motifs_file, tempfile.name)
fimo_scores = {}
for line in fimo_output.splitlines():
parts = line.split("\t")
if len(parts) < 2 or not parts[0].isdigit():
continue
fimo_scores[int(parts[0])] = float(parts[5])
return fimo_scores