for linear gap cost use -l or -linear\n\
for affine gap cost use -a or -affine\n\
- b, a: parameters for gap cost function\n\
b -> constant gap cost or slope when performing linear/affine gap constant (extension penalty)\n\
a -> instersect for affine gap cost (opening gap penalty)\n\
- -o: output alignment. if missing then outputs optimal score")
arguments = GetArguments(sys.argv) # parsing arguments
# print(arguments.seq2)
# print(arguments.score_matrix)
sequences = [arguments.seq1, arguments.seq2]
substitution_matrix = arguments.score_matrix
gap_params = arguments.gap_params
alignmentType = arguments.alignment_type
my_alignment = Alignment(sequences, substitution_matrix, alignmentType, gap_params)
my_alignment.align()
if arguments.output:
print(">seq1")
print(my_alignment.a)
print(">seq2")
print(my_alignment.b)
else:
print(my_alignment.score)
# # Score matrix print
# for row in range(len(T)):
# print(T[row])
