diff --git a/src/g2g b/src/g2g index 03c114e..15e8aec 100755 --- a/src/g2g +++ b/src/g2g @@ -42,6 +42,11 @@ jloh g2g --target --query [options] --ref-B Second FASTA sequence [!] --output-dir Where to place the output files [.] +[mapping] +--default -c 65 -b 200 -l 50 +--sensitive -c 100 -b 50 -l 50 --mum [off] +--relaxed -c 50 -b 200 -l 20 [off] + [parameters] --est-divergence Estimated divergence between the two genomes (0.0-1.0) [0.01] Alignments will be retained up to twice this divergence @@ -56,6 +61,8 @@ p = ap.ArgumentParser() p.add_argument("--ref-A") p.add_argument("--ref-B") p.add_argument("--output-dir", default=".") +p.add_argument("--default", action="store_true", default=True) +p.add_argument("--sensitive", action="store_true", default=False) p.add_argument("--est-divergence", default=0.01, type=float) p.add_argument("--min-length", default=1000, type=int) args = p.parse_args() @@ -68,12 +75,19 @@ def map_genomes(args, tmp_dir): """ # map + if args.default: + params = "-c 65 -b 200 -l 50" + elif args.sensitive: + params = "-c 100 -b 50 -l 50 --mum" + elif args.relaxed: + params = "-c 50 -b 200 -l 20" + out_prefix_A = f"{tmp_dir}/out_A" - cmd = f"nucmer -p {out_prefix_A} -c 100 -b 50 -l 50 --mum {args.ref_A} {args.ref_B}" + cmd = f"nucmer -p {out_prefix_A} {params} {args.ref_A} {args.ref_B}" os.system(cmd) out_prefix_B = f"{tmp_dir}/out_B" - cmd = f"nucmer -p {out_prefix_B} -c 100 -b 50 -l 50 --mum {args.ref_B} {args.ref_A}" + cmd = f"nucmer -p {out_prefix_B} {params} {args.ref_B} {args.ref_A}" os.system(cmd) # min identity = twice the estimated divergence