def main(args=None):
info()
if args is None:
args = sys.argv[1:]
if "-h" in args or "--help" in args:
usage()
sys.exit(2)
if "-id" in args:
run_id = get_arg(args, "-id")
else:
run_id = str(int(time.time())) # use timestamp as unique run identifier
# determine mode (new alignment or redrawing)
if "-redraw" in args:
new_align = False
else:
new_align = True
ensure_dir([g_root_dir, r_root_dir])
for item in dirs.values():
ensure_dir([r_root_dir+run_id+item])
# one-pair or multiple?
if len(genomes) < 2:
raise Exception("ERROR: Need at least two genomes to align!")
elif len(genomes) == 2:
align_pairwise(genomes, new_align, r_root_dir, g_root_dir, dirs, run_id, max_size, chop_mode, mauve_exec, mtype, segtype, min_size)
else:
align_multi(genomes, new_align, r_root_dir, g_root_dir, dirs, run_id, max_size, chop_mode, mauve_exec, mtype, segtype, idpt, fct_flags, fct_colors, min_size)
# prep directories
data_dir = "data/"+argv[1]+"/"
run = argv[2]
dirs = {
'seqfiles': data_dir+"seqfiles/",
'mauve': data_dir+"mauve/"+run+"/",
'aln_segs': data_dir+"seg_aln/",
'maps': data_dir+"maps/"+run+"/"
}
for item in dirs.values():
ensure_dir([item])
# determine mode (new alignment or redrawing)
new_align = True
if len(argv) > 3:
mode = argv[3]
if mode == 'redraw':
new_align = False
# one-pair or multiple?
if len(genomes) < 2:
raise Exception("ERROR: Not enough genomes to align!")
elif len(genomes) == 2:
align_pairwise(genomes, new_align, dirs, run)
else:
align_multi(genomes, new_align, dirs, run)