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)
#from sets.thuricins import zwitter as genomes from sets.pXO2s import pXO2s as genomes # 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: