def test_present_for_all_4():
aligned_dict={}
prt_seq ={}
prt_mapping={}
prt_seq["p1"] = ["A","S","D","B","A","S","X"]
prt_seq["p2"] = ["A","M","D","B","M","A","S","D"]
# 0 1 2 3 4 5 6 7 8 9
aligned_dict["p1"] = ["-","A","S","D","B","-","-","A","S","X"]
aligned_dict["p2"] = ["-","A","M","D","B","-","M","A","S","D"]
prt_mapping["p1"] ={0:1, 1:2, 2:3, 3:4, 4:7, 5:8,6:9}
prt_mapping["p2"] ={0:1, 1:2, 2:3, 3:4, 4:6, 5:7,6:8,7:9}
p1_res=_present_for_all("p1", prt_mapping["p1"], prt_seq["p1"], aligned_dict)
p2_res=_present_for_all("p2", prt_mapping["p2"], prt_seq["p2"], aligned_dict)
assert(p1_res==[2,3,5])
assert(p2_res==[2,3,6])
return
def test_present_for_all_same_seq():
yaml_file = load_yaml_file(os.path.join(base_dir,"mdl_dir","project.yaml"))
aligned_dict={}
for protein in yaml_file["protein_list"]:
t = load_random_traj(yaml_file, protein)
aligned_dict[protein] = t.top.to_fasta(chain=0)
for protein in yaml_file["protein_list"]:
aligned_seq = aligned_dict[protein]
prt_mapping, prt_seq =_map_residue_ind_seq_ind(yaml_file, protein, aligned_seq)
assert(len(_present_for_all(protein, prt_mapping, prt_seq, aligned_dict))==len(prt_seq))
return
def test_present_for_all_2():
aligned_dict={}
prt_seq ={}
prt_mapping={}
prt_seq["p1"] = ["A","S","D","B","A","S","D"]
prt_seq["p2"] = ["A","M","D","B","M","A","S","D"]
# 0 1 2 3 4 5 6 7 8 9
aligned_dict["p1"] = ["A","S","D","B","-","-","A","S","D"]
aligned_dict["p2"] = ["A","M","D","B","-","M","A","S","D"]
prt_mapping["p1"] ={0:0,1:1, 2:2, 3:3, 4:6, 5:7,6:8}
prt_mapping["p2"] ={0:0,1:1, 2:2, 3:3, 4:5, 5:6,6:7, 7:8}
p1_res=_present_for_all("p1", prt_mapping["p1"], prt_seq["p1"], aligned_dict)
p2_res=_present_for_all("p2", prt_mapping["p2"], prt_seq["p2"], aligned_dict)
print(p1_res)
assert(p1_res==[0,2,3,5,6])
assert(p2_res==[0,2,3,6,7])
return
