lib.py

# Asn or Asp / B  AAU, AAC; GAU, GAC
# Gln or Glu / Z  CAA, CAG; GAA, GAG
# START AUG
tt = """Ala / A GCU, GCC, GCA, GCG
Ile / I AUU, AUC, AUA
Arg / R CGU, CGC, CGA, CGG; AGA, AGG
Leu / L CUU, CUC, CUA, CUG; UUA, UUG
Asn / N AAU, AAC
Lys / K AAA, AAG
Asp / D GAU, GAC
Met / M AUG
Phe / F UUU, UUC
Cys / C UGU, UGC
Pro / P CCU, CCC, CCA, CCG
Gln / Q CAA, CAG
Ser / S UCU, UCC, UCA, UCG; AGU, AGC
Glu / E GAA, GAG
Thr / T ACU, ACC, ACA, ACG
Trp / W UGG
Gly / G GGU, GGC, GGA, GGG
Tyr / Y UAU, UAC
His / H CAU, CAC
Val / V GUU, GUC, GUA, GUG
STOP    UAA, UGA, UAG
""".strip()
dec = {}
for t in tt.split("\n"):
  k = t[:len("Val / V")].strip()
  v = t[len("Val / V "):]
  if '/' in k:
    k = k.split("/")[-1].strip()
  k = k.replace("STOP", "*")
  v = v.replace(",", "").replace(";", "").lower().replace("u", "t").split(" ")
  for vv in v:
    if vv in dec:
      print("dup", vv)
    dec[vv.strip()] = k

def translate(x, protein=False):
  x = x.lower()
  aa = []
  for i in range(0, len(x)-2, 3):
    aa.append(dec[x[i:i+3]])
  aa = ''.join(aa)
  if protein:
    if aa[0] != "M" or aa[-1] != "*":
      print("BAD PROTEIN")
      print(aa)
      return None
    aa = aa[:-1]
  return aa

import pathlib
import os
import json
with open(os.path.join(pathlib.Path(__file__).parent.absolute(), "data", "allseq.json")) as f:
  allseq = json.load(f)
cc = allseq['MN908947']