def get_mutation_effects(snp):
cdsSt = snp["cds_st"]
cdsEn = snp["cds_en"]
get_position(snp)
pos = snp["snp_start"]
pos_end = snp["snp_end"]
get_codon_for_snp(snp)
mutations = []
for (newbase, al_freq) in snp["mut_freqs"].items():
ncod = None
naa = None
mut_freq = float(al_freq)*float(snp["ref_freq"])
confs = getSNPpvals(float(snp["hits"]),mut_freq)
(c_het,p_homo) = confs
if pos < cdsSt:
effect = ["5utr"]
elif pos > cdsEn:
effect = ["3utr"]
else:
if newbase == "-" and (pos_end -pos)%3 == 0:
effect = ["deletion", "inframe"]
if newbase == "-" and (pos_end -pos)%3 != 0:
effect = ["deletion", "frameshift"]
elif len(newbase) > 1 and (len(newbase)-1) % 3 != 0:
effect = ["insertion", "frameshift"]
elif len(newbase) > 1 and (len(newbase)-1) % 3 == 0:
effect = ["insertion", "inframe"]
elif newbase == snp["allele"]:
effect = ["reference"]
ncod = snp["codon"]
naa = snpl["aa"]
elif len(newbase) == 1:
effect = []
ofs = snp["offset"]
ocod = snp["codon"]
if ocod.startswith("utr"):
effect.append("untranslated")
ncod=ocod
naa = snp["aa"]
else:
ncod = ocod[0:ofs] + newbase + ocod[ofs+1:3]
naa = codons.translate(ncod)
if naa == snp["aa"]:
effect.append("synonymous")
elif snp["aa"] == "*":
effect.append("runon")
elif naa == "*":
effect.append("nonsense")
else:
effect.append("missense")
mutations.append( { "allele" : newbase,
"codon" : ncod,
"aa" : naa,
"effect" : effect,
"conf_het": c_het,
"p_homo": p_homo,
"frequency": mut_freq,
"mut_map": snp["mut_maps"][newbase] } )
snp["mutations"] = mutations
def get_codon_for_snp(snp):
cdsSt = snp["cds_st"]
cdsEn = snp["cds_en"]
pos = snp["snp_start"]
aa_pos = None
frame = None
codon = None
aa = None
if pos < cdsSt:
codon = "5utr"
elif pos > cdsEn:
codon = "3utr"
else:
codonSt = snp["flank_offset"]
frame = (pos-cdsSt) % 3
aa_pos = (pos-cdsSt)/3
codonSt -= frame
codon = snp["bare_flank"][codonSt:codonSt+3]
aa = codons.translate(codon)
snp["offset"]=frame
snp["codon"]=codon
snp["aa"]=aa
snp["aa_pos"]=aa_pos