diff options
Diffstat (limited to 'pangraph/build.py')
| -rw-r--r-- | pangraph/build.py | 30 |
1 files changed, 24 insertions, 6 deletions
diff --git a/pangraph/build.py b/pangraph/build.py index 01595b7..a29b4fa 100644 --- a/pangraph/build.py +++ b/pangraph/build.py @@ -37,10 +37,24 @@ def register_args(parser): type=int, default=22, help="energy cost for mutations (used during block merges)") + parser.add_argument("-w", "--window", + metavar="edge window", + type=int, + default=1000, + help="amount of sequence to align from for end repair") + parser.add_argument("-e", "--extend", + metavar="edge extend", + type=int, + default=1000, + help="amount of sequence to extend for end repair") parser.add_argument("-s", "--statistics", default=False, action='store_true', help="boolean flag that toggles whether the graph statistics are computed for intermediate graphs") + parser.add_argument("-n", "--num", + type=int, + default=-1, + help="manually sets the tmp directory number. internal use only.") parser.add_argument("input", type=str, default="-", @@ -63,14 +77,17 @@ def main(args): root = args.dir.rstrip('/') tmp = f"{root}/tmp" - i = 0 - while os.path.isdir(tmp) and i < 32: - i += 1 - tmp = f"{root}/tmp{i:03d}" + if args.num == -1: + i = 0 + while os.path.isdir(tmp) and i < 64: + i += 1 + tmp = f"{root}/tmp{i:03d}" + else: + tmp = f"{root}/tmp{args.num:03d}" mkdir(tmp) log("aligning") - T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.statistics) + T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.window, args.extend, args.statistics) # TODO: when debugging phase is done, remove tmp directory graphs = T.collect() @@ -82,6 +99,7 @@ def main(args): with open(f"{root}/graph_{i:03d}.fa", 'w') as fd: g.write_fasta(fd) - T.write_json(sys.stdout, no_seqs=True) + # NOTE: uncomment when done debugging + # T.write_json(sys.stdout, no_seqs=True) return 0 |