def getCodonFromSequence(genomes_rule, map, pos, seq=None):
if not seq:
seq = fetch_mapping_rna(genomes_rule, map)
if pos < 1 or pos > len(seq):
raise Exception( "translate.py:getCodonFromSequence - pos out of range [1,len(sequence)]")
ofst=None
cod_num = None
len5=0
for lexon in map["utr5"]:
len5 += lexon[1]-lexon[0]
lencds = 0
for cexon in map["cds"]:
lencds += cexon[1]-cexon[0]
if pos <= len5:
codon = "utr5"
aa= None
elif pos > len5+lencds:
codon= "utr3"
aa=None
else:
ofst = (pos-len5-1) % 3
cod_num = (pos-len5-1) / 3 + 1
codon = seq[pos-ofst-1:pos-ofst+2]
aa = codons.translate(codon)
base = seq[pos-1]
result = { "mapping_uid": map["uid"],
"pos":pos,
"allele":base,
"codon":codon,
"aa":aa,
"aa_pos":cod_num,
"offset":ofst }
return result
def getMutationEffects(genomes_rule, map, pos, newbases):
if map.has_key("rna"):
seq = map["rna"]
else:
seq = None
original = getCodonFromSequence(genomes_rule, map, pos, seq)
mutations = []
for newbase in newbases:
ncod = None
naa = None
if newbase == "-":
if original["codon"].startswith("utr"):
effect = ["deletion","untranslated"]
else:
effect = ["deletion", "frameshift"]
elif len(newbase) > 1 and (len(newbase)-1) % 3 != 0:
if original["codon"].startswith("utr"):
effect = ["insertion","untranslated"]
else:
effect = ["insertion", "frameshift"]
elif len(newbase) > 1 and (len(newbase)-1) % 3 == 0:
if original["codon"].startswith("utr"):
effect = ["insertion","untranslated"]
else:
effect = ["insertion", "inframe"]
elif newbase == original["allele"]:
effect = ["reference"]
ncod = original["codon"]
naa = original["aa"]
elif len(newbase) == 1:
effect = []
ofs = original["offset"]
ocod = original["codon"]
if ocod.startswith("utr"):
effect.append("untranslated")
ncod=ocod
naa = original["aa"]
else:
ncod = ocod[0:ofs] + newbase + ocod[ofs+1:3]
naa = codons.translate(ncod)
if naa == original["aa"]:
effect.append("synonymous")
elif original["aa"] == "*":
effect.append("runon")
elif naa == "*":
effect.append("nonsense")
else:
effect.append("missense")
mutations.append( { "allele" : newbase,
"codon" : ncod,
"aa" : naa,
"effect" : effect } )
original["mutations"] = mutations
return original
