[estimate] add --multi option; default false

Author: terhorst

smcpp/analysis.py

@@ -418,7 +418,7 @@ def __init__(self, files, args):
         self._init_inference_manager(args.polarization_error)
         self._init_optimizer(args.outdir,
                              args.algorithm, args.xtol, args.ftol,
-                             learn_rho=args.r is None, single=False)
+                             learn_rho=args.r is None, single=not args.multi)
 
 
     def _init_parameters(self, mu, r):
@@ -527,7 +527,7 @@ def __init__(self, files, args):
         self._perform_thinning(args.thinning)
         # Further initialization
         self._init_inference_manager(args.polarization_error)
-        self._init_optimizer(args.outdir, args.algorithm, args.xtol, args.ftol, True)
+        self._init_optimizer(args.outdir, args.algorithm, args.xtol, args.ftol, single=True)
         self._niter = 1
 
     def _validate_data(self):

smcpp/commands/command.py

@@ -58,15 +58,14 @@ def add_common_estimation_args(parser):
                            "from mean heterozygosity",
                       action="store_true", default=False)
     optimizer = parser.add_argument_group("Optimization parameters")
-    optimizer.add_argument(
-        "--no-initialize", action="store_true", default=False, help=argparse.SUPPRESS)
+    optimizer.add_argument("--no-initialize", action="store_true", default=False, help=argparse.SUPPRESS)
     optimizer.add_argument('--em-iterations', type=int,
                            help="number of EM steps to perform", default=20)
     optimizer.add_argument('--algorithm',
                            choices=["BFGS", "L-BFGS-B", "TNC", "AdaMax", "Adam"],
                            default="L-BFGS-B", help=argparse.SUPPRESS)
-    optimizer.add_argument('--blocks', type=int, 
-                           help="number of coordinate ascent blocks. default: min(4, K)")
+    optimizer.add_argument('--multi', default=False, action="store_true",
+                           help="update multiple blocks of coordinates at once")
     optimizer.add_argument("--ftol", type=float,
                            default=smcpp.defaults.ftol,
                            help="stopping criterion for relative improvement in loglik "

test/integration/test.sh

@@ -4,7 +4,7 @@ set -e
 $SMC vcf2smc -v example/example.vcf.gz /tmp/example.1.smc.gz 1 msp1:msp_0,msp_1,msp_2
 $SMC vcf2smc -d msp_0 msp_0 example/example.vcf.gz /tmp/example.2.smc.gz 1 msp2:msp_0,msp_3,msp_4
 $SMC vcf2smc -d msp_1 msp_1 example/example.vcf.gz /tmp/example.12.smc.gz 1 msp1:msp_1,msp_2 msp2:msp_3,msp_4,msp_0
-$SMC estimate -o /tmp/out/1 --unfold --knots 5 --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
+$SMC estimate -o /tmp/out/1 --unfold --knots 5 --multi --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
 $SMC estimate -p 0.01 -r 1e-8 -o /tmp/out/2 --knots 5 --em-iterations 1 1.25e-8 /tmp/example.2.smc.gz
 $SMC split -o /tmp/out/split --em-iterations 1 \
     /tmp/out/1/model.final.json \