Add in Snakemake Log-Files (#147)

* remove double logging

* add in logging redirct

* add in logging redirct
-remove logging from train rule (already performed with parallel)
- remove params.prefix bug from log paths

* bugfix logging redirect for associate.py
- add in logging handlers.clear()
- define logging level

* output additional fields in model_config.yaml , to be used for pretrained_models setup

* adding in logging directive to cv pipeline

* add in log to final regenie pipeline

* fixup! Format Python code with psf/black pull_request

---------

Co-authored-by: PMBio <[email protected]>

deeprvat/cv_utils.py

@@ -16,7 +16,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/data/dense_gt.py

@@ -22,7 +22,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/data/rare.py

@@ -12,7 +12,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/deeprvat/associate.py

@@ -25,10 +25,10 @@
 from tqdm import tqdm, trange
 import zarr
 import re
-
 import deeprvat.deeprvat.models as deeprvat_models
 from deeprvat.data import DenseGTDataset
 
+logging.root.handlers.clear()  # Remove all handlers associated with the root logger object
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
     level=logging.INFO,
@@ -48,6 +48,11 @@
 AGG_FCT = {"mean": np.mean, "max": np.max}
 
 
+@click.group()
+def cli():
+    pass
+
+
 def get_burden(
     batch: Dict,
     agg_models: Dict[str, List[nn.Module]],
@@ -99,11 +104,6 @@ def separate_parallel_results(results: List) -> Tuple[List, ...]:
     return tuple(map(list, zip(*results)))
 
 
-@click.group()
-def cli():
-    pass
-
-
 def make_dataset_(
     config: Dict,
     debug: bool = False,
@@ -306,7 +306,6 @@ def make_regenie_input_(
     gene_metadata_file: Path,
     gtf: Path,
 ):
-    logger.setLevel(logging.INFO)
 
     ## Check options
     if not skip_burdens and burdens_genes_samples is None:
@@ -420,7 +419,7 @@ def make_regenie_input_(
         if average_repeats:
             logger.info("Averaging burdens across all repeats")
             burdens = np.zeros((n_samples, n_genes))
-            for repeat in trange(burdens_zarr.shape[2]):
+            for repeat in trange(burdens_zarr.shape[2], file=sys.stdout):
                 burdens += burdens_zarr[:n_samples, :, repeat]
             burdens = burdens / burdens_zarr.shape[2]
         else:
@@ -448,7 +447,7 @@ def make_regenie_input_(
             n_samples,
             samples=list(sample_ids.astype(str)),
         ) as f:
-            for i in trange(n_genes):
+            for i in trange(n_genes, file=sys.stdout):
                 varid = f"pseudovariant_gene_{ensgids[i]}"
                 this_burdens = burdens[:, i]  # Rescale scores to be in range (0, 2)
                 genotypes = np.stack(
@@ -746,7 +745,7 @@ def load_models(
     }
 
     if len(checkpoint_files[first_repeat]) > 1:
-        logging.info(
+        logger.info(
             f"  Averaging results from {len(checkpoint_files[first_repeat])} models for each repeat"
         )
 
@@ -1064,7 +1063,9 @@ def combine_burden_chunks_(
     end_id = 0
 
     for i, chunk in tqdm(
-        enumerate(range(0, n_chunks)), desc=f"Merging {n_chunks} chunks"
+        enumerate(range(0, n_chunks)),
+        desc=f"Merging {n_chunks} chunks",
+        file=sys.stdout,
     ):
         chunk_dir = burdens_chunks_dir / f"chunk_{chunk}"
 

deeprvat/deeprvat/common_variant_condition_utils.py

@@ -20,7 +20,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/deeprvat/config.py

@@ -16,7 +16,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/deeprvat/evaluate.py

@@ -14,7 +14,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/deeprvat/models.py

@@ -18,7 +18,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/deeprvat/train.py

@@ -9,7 +9,7 @@
 from pprint import pformat, pprint
 from tempfile import TemporaryDirectory
 from typing import Dict, Optional, Tuple, Union
-
+import re
 import click
 import math
 import numpy as np
@@ -37,10 +37,9 @@
 from torch.utils.data import DataLoader, Dataset, Subset
 from tqdm import tqdm
 
-
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)
@@ -872,20 +871,20 @@ def run_bagging(
                 trainer.fit(model, dm)
             except RuntimeError as e:
                 # if batch_size is choosen to big, it will be reduced until it fits the GPU
-                logging.error(f"Caught RuntimeError: {e}")
+                logger.error(f"Caught RuntimeError: {e}")
                 if str(e).find("CUDA out of memory") != -1:
                     if dm.hparams.batch_size > 4:
-                        logging.error(
+                        logger.error(
                             "Retrying training with half the original batch size"
                         )
                         gc.collect()
                         torch.cuda.empty_cache()
                         dm.hparams.batch_size = dm.hparams.batch_size // 2
                     else:
-                        logging.error("Batch size is already <= 4, giving up")
+                        logger.error("Batch size is already <= 4, giving up")
                         raise RuntimeError("Could not find small enough batch size")
                 else:
-                    logging.error(f"Caught unknown error: {e}")
+                    logger.error(f"Caught unknown error: {e}")
                     raise e
             else:
                 break
@@ -1167,7 +1166,21 @@ def best_training_run(
         config = yaml.safe_load(f)
 
     with open(config_file_out, "w") as f:
-        yaml.dump({"model": config["model"]}, f)
+        yaml.dump(
+            {
+                "model": config["model"],
+                "rare_variant_annotations": config["training_data"]["dataset_config"][
+                    "rare_embedding"
+                ]["config"]["annotations"],
+                "training_data_thresholds": {
+                    k: str(re.sub(f"^{k} ", "", v))
+                    for k, v in config["training_data"]["dataset_config"][
+                        "rare_embedding"
+                    ]["config"]["thresholds"].items()
+                },
+            },
+            f,
+        )
 
     n_bags = config["training"]["n_bags"] if not debug else 3
     for k in range(n_bags):

deeprvat/metrics.py

@@ -8,7 +8,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/seed_gene_discovery/evaluate.py

@@ -15,7 +15,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/seed_gene_discovery/seed_gene_discovery.py

@@ -24,7 +24,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

deeprvat/utils.py

@@ -17,7 +17,7 @@
 
 logging.basicConfig(
     format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
-    level="INFO",
+    level=logging.INFO,
     stream=sys.stdout,
 )
 logger = logging.getLogger(__name__)

pipelines/association_testing/association_dataset.snakefile

@@ -16,12 +16,16 @@ rule association_dataset:
     resources:
         mem_mb = lambda wildcards, attempt: 32000 * (attempt + 1),
     priority: 30
+    log:
+        stdout="logs/association_dataset/{phenotype}.stdout", 
+        stderr="logs/association_dataset/{phenotype}.stderr"
     shell:
         'deeprvat_associate make-dataset '
         + debug +
         "--skip-genotypes "
         '{input.data_config} '
-        '{output}'
+        '{output} '
+        + logging_redirct
 
 
 rule association_dataset_burdens:
@@ -33,8 +37,12 @@ rule association_dataset_burdens:
     resources:
         mem_mb = lambda wildcards, attempt: 32000 * (attempt + 1)
     priority: 30
+    log:
+        stdout=f"logs/association_dataset_burdens/{phenotypes[0]}.stdout", 
+        stderr=f"logs/association_dataset_burdens/{phenotypes[0]}.stderr"
     shell:
         'deeprvat_associate make-dataset '
         + debug +
         '{input.data_config} '
-        '{output}'
+        '{output} '
+        + logging_redirct

pipelines/association_testing/burdens.snakefile

@@ -16,12 +16,16 @@ rule combine_burdens:
     threads: 1
     resources:
         mem_mb = lambda wildcards, attempt: 4098 + (attempt - 1) * 4098,
+    log:
+        stdout="logs/combine_burdens/combine_burdens.stdout", 
+        stderr="logs/combine_burdens/combine_burdens.stderr"
     shell:
         ' '.join([
             'deeprvat_associate combine-burden-chunks',
             '{params.prefix}/burdens/chunks/',
             ' --n-chunks ' + str(n_burden_chunks),
-            '{params.prefix}/burdens',
+            '{params.prefix}/burdens ',
+            logging_redirct
         ])
 
 rule all_xy:
@@ -42,14 +46,18 @@ rule compute_xy:
     threads: 8
     resources:
         mem_mb = lambda wildcards, attempt: 20480 + (attempt - 1) * 4098,
+    log:
+        stdout="logs/compute_xy/{phenotype}.stdout", 
+        stderr="logs/compute_xy/{phenotype}.stderr"
     shell:
         ' && '.join([
             ('deeprvat_associate compute-xy '
              '--dataset-file {input.dataset} '
              '{input.data_config} '
              "{output.samples} "
              "{output.x} "
-             "{output.y}")
+             "{output.y} "
+             + logging_redirct)
         ])
 
 
@@ -73,6 +81,9 @@ rule compute_burdens:
     resources:
         mem_mb = 32000,
         gpus = 1
+    log:
+        stdout="logs/compute_burdens/compute_burdens_{chunk}.stdout", 
+        stderr="logs/compute_burdens/compute_burdens_{chunk}.stderr"
     shell:
         ' '.join([
             'deeprvat_associate compute-burdens '
@@ -83,7 +94,8 @@ rule compute_burdens:
             '{input.data_config} '
             '{input.model_config} '
             '{input.checkpoints} '
-            '{params.prefix}/burdens'],
+            '{params.prefix}/burdens '
+            + logging_redirct ],
         )
 
 
@@ -98,11 +110,16 @@ rule reverse_models:
     threads: 4
     resources:
         mem_mb = 20480,
+    log:
+        stdout="logs/reverse_models/reverse_models.stdout", 
+        stderr="logs/reverse_models/reverse_models.stderr"
     shell:
         " && ".join([
             ("deeprvat_associate reverse-models "
              "{input.model_config} "
              "{input.data_config} "
-             "{input.checkpoints}"),
-             "touch {output}"
+             "{input.checkpoints} "
+             + logging_redirct),
+             "touch {output} "
+
         ])