for gene_acid_base in record.attributes["amino_acid"].split("/"):
# get amino acid change
x = gene_acid_base.split(" ",1)
gene = x[0]
amino_acid_change_and_position = x[1]
# starting with F123V, build a list of ways
# this might appear in the PharmGKB data,
# ie. F123V 123F/V Phe123Val 123Phe>Val
acid_changes = []
acid_changes.append(re.sub(r' .*',r'', amino_acid_change_and_position))
acid_changes.append(re.sub(r'([A-Z])(\d+)([A-Z]+)', r'\2\1/\3', acid_changes[0]))
for x in range(2):
acid_changes.append(re.sub(r'[A-Z]', lambda x: codon_123(x.group(0)), acid_changes[x]))
acid_changes[3] = re.sub(r'/', r'>', acid_changes[3])
# query the database
cursor.execute(query, (rs, alleles[0], alleles[1],
gene,
acid_changes[0],
acid_changes[1],
acid_changes[2],
acid_changes[3]))
data = cursor.fetchall()
# if this gene/AA change caused a hit, stop here and report it
if cursor.rowcount > 0:
break
def codon_1to3(aa):
threeletter = codon_123(aa)
if threeletter == "TERM":
threeletter = "Stop"
return threeletter
continue
if rs_number > 0:
found_aa_for_rsid[rs_number] = 1
for gene_acid_base in record.attributes["amino_acid"].split("/"):
# get amino acid change
x = gene_acid_base.split(" ", 1)
gene = x[0]
amino_acid_change_and_position = x[1]
# convert to long form
acid_change = re.sub(r" .*", r"", amino_acid_change_and_position)
acid_change = re.sub(r"[A-Z]", lambda x: codon_123(x.group(0)), acid_change)
acid_change = re.sub(r"TERM", "Stop", acid_change)
# query the database
cursor.execute(query_aa, (gene, acid_change))
data = cursor.fetchall()
# if this gene/AA change caused a hit, stop here and report it
if cursor.rowcount > 0:
break
if cursor.rowcount > 0:
for d in data:
inheritance = d[0]
impact = d[1]
def codon_1to3(aa):
threeletter = codon_123(aa)
if (threeletter == "TERM"):
threeletter = "Stop"
return threeletter
