def run_non_biosynthetic_phmms(fasta: str) -> Dict[str, List[str]]:
""" Finds lanthipeptide-specific domains in the input fasta
Arguments:
fasta: a string containing gene sequences in fasta format
Returns:
a dictionary mapping the hit id to a list of matching query ids
"""
with open(
path.get_full_path(__file__, "data", "non_biosyn_hmms",
"hmmdetails.txt"), "r") as handle:
hmmdetails = [
line.strip().split("\t") for line in handle
if line.count("\t") == 3
]
signature_profiles = [
HmmSignature(details[0], details[1], int(details[2]), details[3])
for details in hmmdetails
]
non_biosynthetic_hmms_by_id = defaultdict(
list) # type: Dict[str, List[str]]
for sig in signature_profiles:
sig.path = path.get_full_path(__file__, "data", "non_biosyn_hmms",
sig.path.rpartition(os.sep)[2])
runresults = subprocessing.run_hmmsearch(sig.path, fasta)
for runresult in runresults:
# Store result if it is above cut-off
for hsp in runresult.hsps:
if hsp.bitscore > sig.cutoff:
non_biosynthetic_hmms_by_id[hsp.hit_id].append(
hsp.query_id)
return non_biosynthetic_hmms_by_id
def run_non_biosynthetic_phmms(cluster_fasta: str) -> Dict[str, List[HSP]]:
""" Try to identify cleavage site using pHMM """
if not cluster_fasta:
return {}
with open(
path.get_full_path(__file__, "data", "non_biosyn_hmms",
"hmmdetails.txt"), "r") as handle:
hmmdetails = [
line.split("\t") for line in handle.read().splitlines()
if line.count("\t") == 3
]
signature_profiles = [
HmmSignature(details[0], details[1], int(details[2]), details[3])
for details in hmmdetails
]
non_biosynthetic_hmms_by_id = defaultdict(list) # type: Dict[str, Any]
for sig in signature_profiles:
sig.path = path.get_full_path(__file__, "data", "non_biosyn_hmms",
sig.path)
runresults = subprocessing.run_hmmsearch(sig.path, cluster_fasta)
for runresult in runresults:
# Store result if it is above cut-off
for hsp in runresult.hsps:
if hsp.bitscore > sig.cutoff:
non_biosynthetic_hmms_by_id[hsp.hit_id].append(hsp)
return non_biosynthetic_hmms_by_id