Add: Allow id_field support for merge_pvalues and create_consensus

segrelab · Dec 1, 2021 · a9f3e92 · a9f3e92
1 parent ae385eb
commit a9f3e92
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Showing 5 changed files with 22 additions and 6 deletions.
diff --git a/micone/pipelines/configs/network_inference.config b/micone/pipelines/configs/network_inference.config
@@ -69,12 +69,15 @@ params {
                 interaction_threshold = 0.3
                 metadata_file = ""
             }
-            // 'merge_pvalues' {}
+            'merge_pvalues' {
+                id_field = "taxid"
+            }
             'create_consensus' {
                 method = 'scaled_sum'
                 parameter = 0.3
                 pvalue_filter = "true"
                 interaction_filter = "true"
+                id_field = "taxid"
             }
         }
     }

diff --git a/micone/pipelines/modules/network_inference/network/create_consensus.nf b/micone/pipelines/modules/network_inference/network/create_consensus.nf
@@ -16,5 +16,6 @@ process create_consensus {
         parameter = params.network_inference.network['create_consensus']['parameter']
         pvalue_filter = params.network_inference.network['create_consensus']['pvalue_filter']
         interaction_filter = params.network_inference.network['create_consensus']['interaction_filter']
+        id_field = params.network_inference.network['create_consensus']['id_field']
         template 'network_inference/network/create_consensus.py'
 }
diff --git a/micone/pipelines/modules/network_inference/network/merge_pvalues.nf b/micone/pipelines/modules/network_inference/network/merge_pvalues.nf
@@ -12,5 +12,6 @@ process merge_pvalues {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        id_field = params.network_inference.network['merge_pvalues']['id_field']
         template 'network_inference/network/merge_pvalues.py'
 }
diff --git a/micone/pipelines/templates/network_inference/network/create_consensus.py b/micone/pipelines/templates/network_inference/network/create_consensus.py
@@ -13,11 +13,12 @@ def main(
     parameter: float,
     pvalue_filter: bool,
     interaction_filter: bool,
+    id_field: str,
 ) -> None:
     networks: List[Network] = []
     for network_file in network_files:
         networks.append(Network.load_json(str(network_file)))
-    network_group = NetworkGroup(networks)
+    network_group = NetworkGroup(networks, id_field=id_field)
     pathlib.Path("consensus/").mkdir(parents=True, exist_ok=True)
     cids = list(range(len(network_group.contexts)))
     filtered_network_group = network_group.filter(
@@ -35,5 +36,14 @@ def main(
     PARAMETER = float("${parameter}")
     PVALUE_FILTER = True if "${pvalue_filter}" == "true" else False
     INTERACTION_FILTER = True if "${interaction_filter}" == "true" else False
+    ID_FIELD = "${id_field}"
     NETWORK_FILES = list(pathlib.Path().glob("*_network.json"))
-    main(BASE_NAME, NETWORK_FILES, METHOD, PARAMETER, PVALUE_FILTER, INTERACTION_FILTER)
+    main(
+        BASE_NAME,
+        NETWORK_FILES,
+        METHOD,
+        PARAMETER,
+        PVALUE_FILTER,
+        INTERACTION_FILTER,
+        ID_FIELD,
+    )
diff --git a/micone/pipelines/templates/network_inference/network/merge_pvalues.py b/micone/pipelines/templates/network_inference/network/merge_pvalues.py
@@ -6,11 +6,11 @@
 from micone import Network, NetworkGroup
 
 
-def main(base_name: str, network_files: List[pathlib.Path]) -> None:
+def main(base_name: str, network_files: List[pathlib.Path], id_field: str) -> None:
     networks: List[Network] = []
     for network_file in network_files:
         networks.append(Network.load_json(str(network_file)))
-    network_group = NetworkGroup(networks)
+    network_group = NetworkGroup(networks, id_field=id_field)
     pathlib.Path("merged/").mkdir(parents=True, exist_ok=True)
     cids = list(range(len(network_group.contexts)))
     merged_network_group = network_group.combine_pvalues(cids)
@@ -21,5 +21,6 @@ def main(base_name: str, network_files: List[pathlib.Path]) -> None:
 
 if __name__ == "__main__":
     BASE_NAME = "merged"
+    ID_FIELD = "${id_field}"
     NETWORK_FILES = list(pathlib.Path().glob("*_network.json"))
-    main(BASE_NAME, NETWORK_FILES)
+    main(BASE_NAME, NETWORK_FILES, ID_FIELD)