bug fix

PMBio · Nov 23, 2023 · 4ad34d1 · 4ad34d1
1 parent 684eb23
commit 4ad34d1
Showing 1 changed file with 84 additions and 84 deletions.
diff --git a/pipelines/training_association_testing.snakefile b/pipelines/training_association_testing.snakefile
@@ -14,7 +14,7 @@ n_repeats = config['n_repeats']
 debug = '--debug ' if debug_flag else ''
 do_scoretest = '--do-scoretest ' if config.get('do_scoretest', False) else ''
 tensor_compression_level = config['training'].get('tensor_compression_level', 1)
-n_parallel_training_jobs = config["training"].get("n_parallel_jobs")
+n_parallel_training_jobs = config["training"].get("n_parallel_jobs", 1)
 
 wildcard_constraints:
     repeat="\d+",
@@ -239,7 +239,7 @@ rule train:
         expand('models/repeat_{repeat}/trial{trial_number}/config.yaml',
                repeat=range(n_repeats), trial_number=range(n_trials)),
         expand('models/repeat_{repeat}/trial{trial_number}/finished.tmp',
-               repeat=range(n_repeats), trial_number=range(n_trials)))
+               repeat=range(n_repeats), trial_number=range(n_trials))
     params:
         phenotypes = " ".join(
             [f"--phenotype {p} "
@@ -248,7 +248,7 @@ rule train:
              f"{p}/deeprvat/y.zarr"
              for p in phenotypes])
     shell:
-        f"parallel --jobs {n_parallel_training_jobs} --results train_repeat{{1}}_trial{{2}}/ "
+        f"parallel --jobs {n_parallel_training_jobs} --results train_repeat{{{{1}}}}_trial{{{{2}}}}/ "
         'deeprvat_train train '
         + debug +
         '--trial-id {{2}} '
@@ -257,89 +257,89 @@ rule train:
         'models/repeat_{{1}}/trial{{2}} '
         "models/repeat_{{1}}/hyperparameter_optimization.db '&&' "
         "touch models/repeat_{{1}}/trial{{2}}/finished.tmp "
-        "::: " + " ".join(range(n_repeats)) + " "
-        "::: " + " ".join(range(n_trials))
+        "::: " + " ".join(map(str, range(n_repeats))) + " "
+        "::: " + " ".join(map(str, range(n_trials)))
 
-rule all_training_dataset:
-    input:
-        input_tensor = expand('{phenotype}/deeprvat/input_tensor.zarr',
-                              phenotype=phenotypes, repeat=range(n_repeats)),
-        covariates = expand('{phenotype}/deeprvat/covariates.zarr',
-                            phenotype=phenotypes, repeat=range(n_repeats)),
-        y = expand('{phenotype}/deeprvat/y.zarr',
-                   phenotype=phenotypes, repeat=range(n_repeats))
+# rule all_training_dataset:
+#     input:
+#         input_tensor = expand('{phenotype}/deeprvat/input_tensor.zarr',
+#                               phenotype=phenotypes, repeat=range(n_repeats)),
+#         covariates = expand('{phenotype}/deeprvat/covariates.zarr',
+#                             phenotype=phenotypes, repeat=range(n_repeats)),
+#         y = expand('{phenotype}/deeprvat/y.zarr',
+#                    phenotype=phenotypes, repeat=range(n_repeats))
 
-rule training_dataset:
-    input:
-        config = '{phenotype}/deeprvat/hpopt_config.yaml',
-        training_dataset = '{phenotype}/deeprvat/training_dataset.pkl'
-    output:
-        input_tensor = directory('{phenotype}/deeprvat/input_tensor.zarr'),
-        covariates = directory('{phenotype}/deeprvat/covariates.zarr'),
-        y = directory('{phenotype}/deeprvat/y.zarr')
-    threads: 8
-    priority: 50
-    shell:
-        (
-            'deeprvat_train make-dataset '
-            + debug +
-            '--compression-level ' + str(tensor_compression_level) + ' '
-            '--training-dataset-file {input.training_dataset} '
-            '{input.config} '
-            '{output.input_tensor} '
-            '{output.covariates} '
-            '{output.y}'
-        )
+# rule training_dataset:
+#     input:
+#         config = '{phenotype}/deeprvat/hpopt_config.yaml',
+#         training_dataset = '{phenotype}/deeprvat/training_dataset.pkl'
+#     output:
+#         input_tensor = directory('{phenotype}/deeprvat/input_tensor.zarr'),
+#         covariates = directory('{phenotype}/deeprvat/covariates.zarr'),
+#         y = directory('{phenotype}/deeprvat/y.zarr')
+#     threads: 8
+#     priority: 50
+#     shell:
+#         (
+#             'deeprvat_train make-dataset '
+#             + debug +
+#             '--compression-level ' + str(tensor_compression_level) + ' '
+#             '--training-dataset-file {input.training_dataset} '
+#             '{input.config} '
+#             '{output.input_tensor} '
+#             '{output.covariates} '
+#             '{output.y}'
+#         )
 
-rule training_dataset_pickle:
-    input:
-        '{phenotype}/deeprvat/hpopt_config.yaml'
-    output:
-        '{phenotype}/deeprvat/training_dataset.pkl'
-    threads: 1
-    shell:
-        (
-            'deeprvat_train make-dataset '
-            '--pickle-only '
-            '--training-dataset-file {output} '
-            '{input} '
-            'dummy dummy dummy'
-        )
+# rule training_dataset_pickle:
+#     input:
+#         '{phenotype}/deeprvat/hpopt_config.yaml'
+#     output:
+#         '{phenotype}/deeprvat/training_dataset.pkl'
+#     threads: 1
+#     shell:
+#         (
+#             'deeprvat_train make-dataset '
+#             '--pickle-only '
+#             '--training-dataset-file {output} '
+#             '{input} '
+#             'dummy dummy dummy'
+#         )
 
-rule all_config:
-    input:
-        seed_genes = expand('{phenotype}/deeprvat/seed_genes.parquet',
-                            phenotype=phenotypes),
-        config = expand('{phenotype}/deeprvat/hpopt_config.yaml',
-                        phenotype=phenotypes),
-        baseline = expand('{phenotype}/deeprvat/baseline_results.parquet',
-                          phenotype=phenotypes),
+# rule all_config:
+#     input:
+#         seed_genes = expand('{phenotype}/deeprvat/seed_genes.parquet',
+#                             phenotype=phenotypes),
+#         config = expand('{phenotype}/deeprvat/hpopt_config.yaml',
+#                         phenotype=phenotypes),
+#         baseline = expand('{phenotype}/deeprvat/baseline_results.parquet',
+#                           phenotype=phenotypes),
 
-rule config:
-    input:
-        config = 'config.yaml',
-        baseline = lambda wildcards: [
-            str(Path(r['base']) / wildcards.phenotype / r['type'] /
-                'eval/burden_associations.parquet')
-            for r in config['baseline_results']
-        ]
-    output:
-        seed_genes = '{phenotype}/deeprvat/seed_genes.parquet',
-        config = '{phenotype}/deeprvat/hpopt_config.yaml',
-        baseline = '{phenotype}/deeprvat/baseline_results.parquet',
-    threads: 1
-    params:
-        baseline_results = lambda wildcards, input: ''.join([
-            f'--baseline-results {b} '
-            for b in input.baseline
-        ])
-    shell:
-        (
-            'deeprvat_config update-config '
-            '--phenotype {wildcards.phenotype} '
-            '{params.baseline_results}'
-            '--baseline-results-out {output.baseline} '
-            '--seed-genes-out {output.seed_genes} '
-            '{input.config} '
-            '{output.config}'
-        )
+# rule config:
+#     input:
+#         config = 'config.yaml',
+#         baseline = lambda wildcards: [
+#             str(Path(r['base']) / wildcards.phenotype / r['type'] /
+#                 'eval/burden_associations.parquet')
+#             for r in config['baseline_results']
+#         ]
+#     output:
+#         seed_genes = '{phenotype}/deeprvat/seed_genes.parquet',
+#         config = '{phenotype}/deeprvat/hpopt_config.yaml',
+#         baseline = '{phenotype}/deeprvat/baseline_results.parquet',
+#     threads: 1
+#     params:
+#         baseline_results = lambda wildcards, input: ''.join([
+#             f'--baseline-results {b} '
+#             for b in input.baseline
+#         ])
+#     shell:
+#         (
+#             'deeprvat_config update-config '
+#             '--phenotype {wildcards.phenotype} '
+#             '{params.baseline_results}'
+#             '--baseline-results-out {output.baseline} '
+#             '--seed-genes-out {output.seed_genes} '
+#             '{input.config} '
+#             '{output.config}'
+#         )