class MaService(object):
HOST = "mutationassessor.org"
ISSUE_UNKNOWN_ID_TYPE = re.compile(r"unknown ID type")
ISSUE_REFERENCE_ALLELE = re.compile(r"reference allele: ([ACGT])")
def __init__(self, assembly, cache_path=None, max_retries=3, max_freq=3):
self.assembly = assembly
self.cache_path = cache_path
self.__restful = Request(max_retries=max_retries, max_freq=max_freq)
def get(self, chr, strand, start, ref, alt, var_id=None):
done = False
while not done:
response = self.__restful.get("http://{0}/".format(self.HOST),
params={
"cm" : "var",
"var" : "{0},{1},{2},{3},{4}".format(self.assembly, chr, start, ref, alt),
"frm" : "txt",
"fts" : "all"
})
if response is None:
return None
hdr = response.readline().rstrip("\n").split("\t")
fields = response.readline().rstrip("\n").split("\t")
hlen = len(hdr)
if hlen == 0 or hlen != len(fields):
return None
r = {}
for i in range(hlen):
r[hdr[i]] = fields[i] if len(fields[i]) > 0 else None
mapping_issue = r["Mapping issue"]
if mapping_issue is not None:
if self.ISSUE_UNKNOWN_ID_TYPE.match(mapping_issue):
return None
m = self.ISSUE_REFERENCE_ALLELE.match(mapping_issue)
if m is not None:
ref = m.group(1)
strand = {"+" : "-", "-" : "+"}[strand]
continue
#TODO check: raise Exception("Infinite mapping issue for reference allele")
done = True
uniprot=r["Uniprot"]
fi_score=cast_type(r["FI score"], float)
snps_pos=r["SNPs@position"]
if uniprot is not None or fi_score is not None or snps_pos is not None:
return MaResult(
var_id=var_id, chr=chr, start=start, ref=ref, alt=alt,
uniprot=uniprot, fi_score=fi_score, snps_pos=snps_pos)
else:
return None
def close(self):
pass
def __init__(self, cache_path, max_retries=3, max_freq=3): self.cache_path = cache_path self.results_path = None self.__restful = Request(max_retries=max_retries, max_freq=max_freq)
def __init__(self, assembly, cache_path=None, max_retries=3, max_freq=3): self.assembly = assembly self.cache_path = cache_path self.__restful = Request(max_retries=max_retries, max_freq=max_freq)
class VepService(object):
HOST = "beta.rest.ensembl.org"
VEP_STRAND = { "+" : "1", "-" : "-1", "1" : "1", "-1" : "-1" }
def __init__(self, cache_path, max_retries=3, max_freq=3):
self.cache_path = cache_path
self.results_path = None
self.__restful = Request(max_retries=max_retries, max_freq=max_freq)
def __parse_response(self, var_id, chr, start, end, strand, alt, response):
root = json.load(response)
if not isinstance(root, dict):
raise Exception("Unexpected result from VEP web service:\n{0}".format(json.dumps(root)))
results = []
found = set()
tag = ":".join([chr, str(start), str(end), strand, alt])
for data in root["data"]:
#chromosome = data["location"]["name"];
#start = data["location"]["start"];
for trans in data["transcripts"]:
gene = trans.get("gene_id");
transcript = trans.get("transcript_id")
tstart = trans.get("translation_start")
tend = trans.get("translation_end")
if tstart is not None and tend is not None and tstart != tend:
protein_pos = "{0}-{1}".format(tstart, tend)
elif tstart is not None:
protein_pos = tstart
elif tend is not None:
protein_pos = tend
else:
protein_pos = None
protein = trans.get("translation_stable_id")
for allele in trans.get("alleles", []):
consequences = allele.get("consequence_terms")
#allele_string = allele["allele_string"]
aa_change = allele.get("pep_allele_string")
sift_score = allele.get("sift_score")
polyphen_score = allele.get("polyphen_score")
key = "{0}|{1}".format(tag, transcript)
if key not in found:
found.add(key)
results += [VepResult(
var_id=var_id, chr=chr, start=start, allele=allele,
gene=gene, transcript=transcript, consequences=consequences,
protein_pos = protein_pos, aa_change=aa_change, protein=protein,
sift=sift_score, polyphen=polyphen_score)]
return results
def get(self, chr, start, end, strand, alt, var_id=None):
strand = self.VEP_STRAND[strand]
url = "http://{0}/vep/human/{1}:{2}-{3}:{4}/{5}/consequences".format(
self.HOST, chr, start, end, strand, alt)
response = self.__restful.get(url, headers={"Content-type" : "application/json"})
if response is None:
return None
return self.__parse_response(var_id, chr, start, end, strand, alt, response)
def run(self, variants_path):
"""
Run the VEP service and save results in a temporary file.
:param variants_path: File with variants. In BED format. http://www.ensembl.org/info/docs/variation/vep/vep_script.html#custom_formats
:return: True if successfull or False otherwise
"""
if self.results_path is None:
self.results_path = tempfile.mkstemp()[1]
with open(self.results_path, "w") as rf:
with open(variants_path, "r") as vf:
column_types = (str, int, int, str, str, int)
for fields in tsv.lines(vf, column_types):
chr, start, end, allele, strand, var_id = fields
alt = allele[allele.find("/") + 1:]
results = self.get(chr, start, end, strand, alt, var_id)
if results is None:
continue
for r in results:
rf.write(tsv.line_text(
var_id, chr, start, allele,
r.gene, r.transcript, ",".join(sorted(r.consequences)),
r.protein_pos, r.aa_change, r.protein,
r.sift, r.polyphen, null_value="-"))
def results(self):
"""
Iterator that parses the results temporary file and yields VepResult's
"""
with open(self.results_path, "r") as f:
column_types = (int, str, int, str, str, str, _ctype, str, str, str, float, float)
for fields in tsv.lines(f, column_types, null_value="-"):
var_id, chr, start, allele, gene, transcript, consequences, protein_pos, aa_change, protein, sift, polyphen = fields
yield VepResult(var_id=var_id, chr=chr, start=start, allele=allele,
gene=gene, transcript=transcript, consequences=consequences,
protein_pos = protein_pos, aa_change=aa_change, protein=protein,
sift=sift, polyphen=polyphen)
def close(self):
"""
Removes temporary files
"""
if self.results_path is not None:
os.remove(self.results_path)
self.results_path = None
