bella-companion 0.0.17__py3-none-any.whl → 0.0.19__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 changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
+            f"-D predictorFiles={all_predictor_files}",
+        ]
+    )
+    flight_predictor_data = " ".join(
+        [
+            f"-D msa_file={msa_file}",
+            f"-D changeTimesFile={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}/results.py

@@ -10,7 +10,7 @@ from phylogenie import get_node_depths, load_newick
 
 def _plot_predictions(output_dir: Path):
     log_summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"])
-    log_summary = pl.read_csv(log_summaries_dir / "fbd-empirical" / "MLP.csv")
+    log_summary = pl.read_csv(log_summaries_dir / "platyrrhine" / "MLP.csv")
 
     data_dir = Path(__file__).parent / "data"
     change_times = (
@@ -63,7 +63,7 @@ def _plot_predictions(output_dir: Path):
         plt.close()
 
 
-def plot_fbd_empirical_results():
-    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-empirical"
+def plot_platyrrhine_results():
+    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "platyrrhine"
     os.makedirs(output_dir, exist_ok=True)
     _plot_predictions(output_dir)

bella_companion/{fbd_empirical → platyrrhine}/run_beast.py

@@ -12,7 +12,7 @@ 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 / "fbd-empirical"
+    output_dir = base_output_dir / "platyrrhine"
     os.makedirs(output_dir, exist_ok=True)
 
     data_dir = Path(__file__).parent / "data"
@@ -64,9 +64,9 @@ def run_beast():
         )
         job_ids[i] = submit_job(
             command,
-            Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "fbd-empirical" / str(i),
+            Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "platyrrhine" / str(i),
             mem_per_cpu="12000",
         )
 
-    with open(base_output_dir / "fbd_empirical_job_ids.json", "w") as f:
+    with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:
         json.dump(job_ids, f)

bella_companion/{fbd_empirical → platyrrhine}/summarize_logs.py

@@ -12,7 +12,7 @@ def summarize_logs():
     change_times = pl.read_csv(data_dir / "change_times.csv", has_header=False)
     n_time_bins = len(change_times) + 1
 
-    logs_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"]) / "fbd-empirical"
+    logs_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"]) / "platyrrhine"
     summaries = summarize_logs_dir(
         logs_dir=logs_dir,
         target_columns=[
@@ -24,7 +24,7 @@ def summarize_logs():
     )
     weights = read_weights_dir(logs_dir)
 
-    summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"], "fbd-empirical")
+    summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"], "platyrrhine")
     os.makedirs(summaries_dir, exist_ok=True)
     summaries.write_csv(summaries_dir / "MLP.csv")
     joblib.dump(weights, summaries_dir / "MLP.weights.pkl")

{bella_companion-0.0.17.dist-info → bella_companion-0.0.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.17
+Version: 0.0.19
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com
@@ -12,5 +12,5 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: arviz (>=0.22.0,<0.23.0)
 Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
 Requires-Dist: dotenv (>=0.9.9,<0.10.0)
-Requires-Dist: phylogenie (>=3.1.1,<4.0.0)
+Requires-Dist: phylogenie (>=3.1.2,<4.0.0)
 Requires-Dist: seaborn (>=0.13.2,<0.14.0)

{bella_companion-0.0.17.dist-info → bella_companion-0.0.19.dist-info}/RECORD

@@ -1,13 +1,34 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=D-kQuj0I-g5Vm5-mXdOZoio68mhOBpJ3jVG8B2Kwvn4,2190
-bella_companion/fbd_empirical/__init__.py,sha256=FgzjaEpwZImvBsJs17ghF0ltZvhFmgmkTGGF3HgdsGo,284
-bella_companion/fbd_empirical/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
-bella_companion/fbd_empirical/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
-bella_companion/fbd_empirical/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
-bella_companion/fbd_empirical/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
-bella_companion/fbd_empirical/results.py,sha256=GiODVJNzSa2Qws_KSoKwbXW6nkpWpcJqi43XVxXFj4M,2562
-bella_companion/fbd_empirical/run_beast.py,sha256=60t8tbqlgdv86JwBk_DvUQ8i7TpThz0EmwEv-OkBAQM,2560
-bella_companion/fbd_empirical/summarize_logs.py,sha256=f3NgdyrCmbD5eHDHYwiA8ggh4b3rZ63SrlfDt0FAZmc,955
+bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
+bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
+bella_companion/eucovid/beast_configs/GLM.xml,sha256=ng13sapf8qe1OGm3xSjl-N_4Fa0gWEOPU172z2XpyQM,11731
+bella_companion/eucovid/beast_configs/MLP.xml,sha256=4niHx3FmSsmKyDv9eNS1g9cZ6ShHbWjzXIbfg8pQa-k,11347
+bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=oDOxiXPlL5zwuvyOPkdZmdSprivYNbDScjT1IvWnZFI,11548
+bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
+bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
+bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
+bella_companion/eucovid/data/osi.tsv,sha256=iTDWL_-PnVQPg_-hWROXWKNFakDq_S1fEig1A_MqMVI,9228
+bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv,sha256=5gP-cEzgKSCvlK0_PlkrimYGEwOaLPO0GiiM4PIKU-M,280
+bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv,sha256=rr71QPiJu35CYbySMJyH_GDX51D2iTIncZImwAXIvlo,1890
+bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv,sha256=5WztZpQrjK7puERA1oxsCn5t2G1w9NGTGKjr85gMQ54,1873
+bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv,sha256=qfRTXyZItzEm8pxurhFYO-DvpJXD-J4lMH5eyZKF0aE,1862
+bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv,sha256=kke2eHlVuc84qMj1WBllhBG2BQt7JHUWDZeiVoAP8Lw,1900
+bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv,sha256=5YDXe4GstyyRKP15213cAAEm5lVFW_bC98R8ipc1XoE,1900
+bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv,sha256=3fVYRQ1ylwsa7YptMU8f_xELwwqIF3Ux8akL9UaXKis,1904
+bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv,sha256=Ku39Ts0HW9r5lThAZ01V7HJDi0aoRYs0aQs5EXlZCkQ,1904
+bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5DIaZuc3B0mSs-B3kw3G2zja1LfmL_xLwlNtLDo,280
+bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
+bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
+bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
+bella_companion/eucovid/run_beast.py,sha256=L_Ng1kG8o94kK3HNeVj1Yq6FsPjolGWWxfnxRrcQeu0,3662
+bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
+bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
+bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
+bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
+bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
+bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
+bella_companion/platyrrhine/run_beast.py,sha256=caUmebyZMzOukI8RdOlECsT3DStShi0NZNzEJ72qAaw,2554
+bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
 bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
 bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
 bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=J-OVblMRmk4XRhz9DHhLpMwaIzqSqYZ7Yq7dTMvQW1s,4094
@@ -48,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
 bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
 bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
 bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
-bella_companion-0.0.17.dist-info/METADATA,sha256=qYxYfMIkltCBPnEyG1eOLKHwZV3vQPZjG9phWbZeGvw,576
-bella_companion-0.0.17.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.17.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.17.dist-info/RECORD,,
+bella_companion-0.0.19.dist-info/METADATA,sha256=xTGQXsmCvuL4RhWlp5-EmPs1vQWApd-A11r-ICeUmxo,576
+bella_companion-0.0.19.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.19.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.19.dist-info/RECORD,,

bella_companion/fbd_empirical/__init__.py

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