def dinuc_shuffling_generator(argu):
seqs, fg_gc_list, fg_lengths = get_seqs(argu.fg_file)
bg_gc_list, bg_lengths = dinuc_shuff.generate_sequences(seqs, argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Generated background", "GC", "\nGC plot")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Generated background", "Len", "\nLength plot")
def dinuc_shuffling_generator(argu):
seqs, fg_gc_list, fg_lengths = get_seqs(argu.fg_file)
bg_gc_list, bg_lengths = dinuc_shuff.generate_sequences(seqs, argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Generated background", "GC", "\nGC plot")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Generated background", "Len", "\nLength plot")
def main():
args = sys.argv
utils.validate_input(args)
sub_matrix_path, seqs_paths = utils.split_input(args)
sub_matrix = utils.read_scoring_matrix(sub_matrix_path)
alphabet = utils.read_alphabet(sub_matrix_path)
seqs_dict = utils.get_seqs(seqs_paths)
i = 0
for id1, seq1 in seqs_dict.items():
j = 0
for id2, seq2 in seqs_dict.items():
if i < j:
timestart = datetime.now()
hsps = utils.find_hsps(k, T, sub_matrix, seq1, seq2, alphabet)
msps = utils.extend_hsps_to_msps(hsps, sub_matrix, seq1, seq2, X)
graph = utils.gen_graph(msps)
score = utils.runDAG(graph)
timedelta = datetime.now() - timestart
utils.update_output_file(id1, id2, score)
print(f"({id1}, {id2}):\t{timedelta}\t msps: {len(msps)}")
j += 1
i += 1
def dinuc_shuffling_window_generator(argu):
seqs, _, _ = get_seqs(argu.fg_file)
_, _ = dinuc_win_shuff.generate_sequences(seqs, argu.winlen, argu.step,
argu.nfold)
def dinuc_shuffling_generator(argu):
seqs, _, _ = get_seqs(argu.fg_file)
_, _ = dinuc_shuff.generate_sequences(seqs, argu.nfold)
def dinuc_shuffling_window_generator(argu):
seqs, _, _ = get_seqs(argu.fg_file)
_, _ = dinuc_win_shuff.generate_sequences(seqs, argu.winlen, argu.step,
argu.nfold)
def dinuc_shuffling_generator(argu):
seqs, _, _ = get_seqs(argu.fg_file)
_, _ = dinuc_shuff.generate_sequences(seqs, argu.nfold)