def _create_cdna_variant(self):
start = hgvs.location.SimplePosition(118898437)
end = hgvs.location.SimplePosition(118898437)
iv = hgvs.location.Interval(start=start, end=end)
edit = hgvs.edit.NARefAlt(ref="C", alt="T")
posedit = hgvs.posedit.PosEdit(pos=iv, edit=edit)
genomic_variant = hgvs.sequencevariant.SequenceVariant(
ac="NC_000011.9",
type="g",
posedit=posedit, )
variantmapper = hgvs.variantmapper.VariantMapper(self.hdp)
return variantmapper.g_to_c(genomic_variant, "NM_001164277.1")
def getHgvsInfo(pos, var_g_p, txInfoList, chrAc, hdpConnexion):
txExonsList = hdpConnexion.get_tx_exons(txInfoList[3], chrAc, 'splign')
variantmapper = hgvs.variantmapper.EasyVariantMapper(hdpConnexion, primary_assembly='GRCh37')
minDist = None
for exonList in txExonsList:
dist = min(abs(pos - exonList[8]), abs(pos - exonList[9]))
if minDist == None: # initialisation
minDist = dist
exonNum = int(exonList[5]) + 1
else:
if dist < minDist:
minDist = dist
exonNum = int(exonList[5]) + 1
var_c_p = variantmapper.g_to_c(var_g_p, txInfoList[3])
return var_c_p, exonNum, minDist
replace_reference=True)
for var in xrange(len(START)):
if variants_table['variant_type'][var] == "snv":
# create HGVS_g
hgvs_g = assembly + ":" + "g" + "." + str(
START[var]) + REF[var] + ">" + ALT[var]
print("Converting: " + str(hgvs_g))
#hp = hgvs.parser.Parser()
var_g = hp.parse_hgvs_variant(hgvs_g)
transcripts = variantmapper.relevant_transcripts(var_g)
var_c = variantmapper.g_to_c(var_g, 'NM_000546.5')
var_p = variantmapper.c_to_p(var_c)
# create final table
final_table.loc[var].Chr = "17"
final_table.loc[var].Start = START[var]
final_table.loc[var].End = END[var]
final_table.loc[var].Ref = REF[var]
final_table.loc[var].Alt = ALT[var]
final_table.loc[var].HGVS_g = var_g
final_table.loc[var].HGVS_c = var_c
final_table.loc[var].HGVS_p = var_p
else:
# create HGVS_g
variant_type = str(variants_table['variant_type'][var])