bella-companion 0.0.16__py3-none-any.whl → 0.0.18__py3-none-any.whl

bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv

@@ -0,0 +1,6 @@
+0.019125683060110532
+0.057377049180331596
+0.0983606557379062
+0.12295081967226906
+0.1420765027323796
+0.18306010928972682

bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv

@@ -0,0 +1,3 @@
+0.019125683060110532
+0.0983606557379062
+0.18306010928972682

bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv

@@ -0,0 +1,20 @@
+-1.3405299471	-1.345806766	-1.3512072478	-1.3448952046
+-1.040355107	-0.0881656333	-0.4582081333	1.0712567879
+-1.0351370181	-0.2281786725	-0.4494345583	1.2186350836
+-1.3512072478	-0.3613020502	-0.2354915099	0.5261323835
+-1.2405584625	0.2198152275	0.5320931776	-0.3818162253
+-1.3146740757	-1.3211624933	-1.3512072478	-1.3050486897
+-0.9401276287	0.4036780489	0.524890239	1.561202424
+-0.9527207215	0.2509108009	0.4583245048	1.7568044456
+-1.3368793783	0.6153635605	0.676014604	1.6911556787
+-1.1536256133	0.6242106372	0.924551832	0.6534556808
+-1.2293447841	-1.2183082911	-1.284435751	-1.0455195408
+-0.3334656741	0.4068453606	0.5550254535	1.5299700031
+-0.4472959305	0.2260837023	0.472758401	1.7126046255
+-0.5674230736	0.6579311005	0.7199273173	1.7312050096
+-0.5714216646	0.752964957	1.0273007955	0.8297001311
+-1.2397477985	-1.2555826444	-1.3025435133	-1.1159647011
+-0.2764997718	0.4125068998	0.6005798788	1.5818044584
+-0.3781670831	0.2838430455	0.553443893	1.8181907424
+-0.5085841919	0.6841126877	0.7369465342	1.7862369916
+-0.499497862	0.6774213601	0.9790687736	0.7565746699

bella_companion/eucovid/run_beast.py

@@ -0,0 +1,111 @@
+import json
+import os
+from glob import glob
+from pathlib import Path
+
+from bella_companion.utils import submit_job
+
+
+def run_beast():
+    base_output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
+    output_dir = base_output_dir / "eucovid"
+    os.makedirs(output_dir, exist_ok=True)
+
+    base_log_dir = Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "eucovid"
+
+    data_dir = Path(__file__).parent / "data"
+    beast_configs_dir = Path(__file__).parent / "beast_configs"
+    msa_file = data_dir / "msa.fasta"
+
+    predictors_dir = data_dir / "predictors"
+    all_predictor_files = ",".join(glob(str(predictors_dir / "all" / "*.tsv")))
+    all_predictors_data = " ".join(
+        [
+            f"-D msa_file={msa_file}",
+            f"-D changeTimes={predictors_dir / 'changetimes_all_7e.tsv'}",
+            f"-D predictorFiles={all_predictor_files}",
+        ]
+    )
+    flight_predictor_data = " ".join(
+        [
+            f"-D msa_file={msa_file}",
+            f"-D changeTimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
+            f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
+        ]
+    )
+
+    job_ids = {}
+
+    os.makedirs(output_dir / "Nonparametric", exist_ok=True)
+    job_ids["Nonparametric"] = submit_job(
+        " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D msa_file={msa_file}",
+                f"-prefix {output_dir / 'Nonparametric'}{os.sep}",
+                str(beast_configs_dir / "Nonparametric.xml"),
+            ]
+        ),
+        base_log_dir / "Nonparametric",
+    )
+
+    os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
+    job_ids["all-predictors-GLM"] = submit_job(
+        " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D ReDimension='{5 * 7}'",
+                all_predictors_data,
+                f"-prefix {output_dir / 'all-predictors-GLM'}{os.sep}",
+                str(beast_configs_dir / "GLM.xml"),
+            ]
+        ),
+        base_log_dir / "all-predictors-GLM",
+    )
+
+    os.makedirs(output_dir / "flights-GLM", exist_ok=True)
+    job_ids["flights-GLM"] = submit_job(
+        " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D ReDimension='{5 * 4}'",
+                flight_predictor_data,
+                f"-prefix {output_dir / 'flights-GLM'}{os.sep}",
+                str(beast_configs_dir / "GLM.xml"),
+            ]
+        ),
+        base_log_dir / "flights-GLM",
+    )
+
+    os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
+    job_ids["all-predictors-MLP"] = submit_job(
+        " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D ReDimension='{5 * 7}'",
+                f'-D layersRange="0,1,2",nodes="16 8"',
+                all_predictors_data,
+                f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}",
+                str(beast_configs_dir / "MLP.xml"),
+            ]
+        ),
+        base_log_dir / "all-predictors-MLP",
+    )
+
+    os.makedirs(output_dir / "flights-MLP", exist_ok=True)
+    job_ids["flights-MLP"] = submit_job(
+        " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D ReDimension='{5 * 4}'",
+                f'-D layersRange="0,1,2",nodes="16 8"',
+                flight_predictor_data,
+                f"-prefix {output_dir / 'flights-MLP'}{os.sep}",
+                str(beast_configs_dir / "MLP.xml"),
+            ]
+        ),
+        base_log_dir / "flights-MLP",
+    )
+
+    with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
+        json.dump(job_ids, f)

bella_companion/platyrrhine/__init__.py

@@ -0,0 +1,5 @@
+from bella_companion.platyrrhine.results import plot_platyrrhine_results
+from bella_companion.platyrrhine.run_beast import run_beast
+from bella_companion.platyrrhine.summarize_logs import summarize_logs
+
+__all__ = ["plot_platyrrhine_results", "run_beast", "summarize_logs"]

bella_companion/{fbd_empirical → platyrrhine}/beast_config.xml

@@ -72,7 +72,7 @@
                         <removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
                         <rhoSampling spec="TimedParameter" values="0.44" times="$(processLength)" typeSet="@typeSet"/>
                     </parameterization>
-					<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
+                    <startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
                 </distribution>
             </distribution>