def return_UPGMA_working(seq_list, names_list, protdist_outfile,
pylip_temps_path):
'''
with protdist
:param seq_list: list of sequence for the UPGMA
:param names_list: the name of the sequences at seq_list, at the same order
:return: UPGMA tree
'''
#protdist_outfile = "protdist_outfile.ph"
mafft_and_phylip.runIt(
names_list, seq_list, protdist_outfile, pylip_temps_path
) #to uncomment when really ranning the tool on the server
matrix = make_initiale_matrix_from_protdist(protdist_outfile)
#print(matrix)
distance_matrix = make_distance_matrix(names_list, matrix)
return make_UPGMA(distance_matrix), distance_matrix
def return_UPGMA(seq_list, names_list, protdist_outfile, pylip_temps_path):
'''
with protdist
:param seq_list: list of sequence for the UPGMA
:param names_list: the name of the sequences at seq_list, at the same order
:return: UPGMA tree
'''
#protdist_outfile = "protdist_outfile.ph"
new_names_list = list()
for i in range(len(names_list)):
new_names_list.append("GG" + str(i)) #for the regex
#print(new_names_list)
mafft_and_phylip.runIt(
new_names_list, seq_list, protdist_outfile, pylip_temps_path
) #to uncomment when really ranning the tool on the server
matrix = make_initiale_matrix_from_protdist(protdist_outfile)
#print(matrix)
distance_matrix = make_distance_matrix(names_list, matrix)
return make_UPGMA(distance_matrix), distance_matrix