Fix: Bugs in network_inference.direct.flashweave pipeline

segrelab · Feb 16, 2021 · 4100643 · 4100643
1 parent 9a9b9a5
commit 4100643
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Showing 3 changed files with 11 additions and 4 deletions.
diff --git a/micone/pipelines/envs/micone-flashweave/env.yml b/micone/pipelines/envs/micone-flashweave/env.yml
@@ -6,3 +6,6 @@ channels:
 dependencies:
     - python=3.8
     - pip>=20.2.4
+    - pip:
+        - pandas>=1.2.1
+        - networkx>=2.5
diff --git a/micone/pipelines/src/network_inference/direct/flashweave/processes/export_gml.py b/micone/pipelines/src/network_inference/direct/flashweave/processes/export_gml.py
@@ -16,9 +16,9 @@ def main(otu_file, network_file, output_file):
     directed = nx.is_directed(graph)
     for source, target, data in graph.edges(data=True):
         if (source in nodes) and (target in nodes):
-            interaction_table[source, target] = data["weight"]
+            interaction_table.loc[source, target] = data["weight"]
             if not directed:
-                interaction_table[target, source] = data["weight"]
+                interaction_table.loc[target, source] = data["weight"]
     interaction_table.to_csv(output_file, sep="\\t", index=True, float_format="%.4f")
 
 

diff --git a/micone/pipelines/src/network_inference/direct/flashweave/processes/flashweave.jl b/micone/pipelines/src/network_inference/direct/flashweave/processes/flashweave.jl
@@ -10,9 +10,13 @@ using DataFrames
 
 # data
 data_path = "${otu_file}"
+new_data_path = "${otu_file.baseName}.tsv"
+if data_path != new_data_path
+    cp(data_path, new_data_path, force=true, follow_symlinks=true)
+end
 metadata_path = "${sample_metadata}"
 metadata = CSV.read(metadata_path, DataFrame; transpose=true)
-new_metadata_path = "transposed_" * metadata_path
+new_metadata_path = "${sample_metadata.baseName}_transposed.tsv"
 CSV.write(new_metadata_path, metadata; delim="\\t")
 
 # options
@@ -21,7 +25,7 @@ heterogeneous = ${heterogeneous}
 FDR = ${fdr_correction}
 
 netw_results = learn_network(
-data_path,
+new_data_path,
 new_metadata_path,
 sensitive=sensitive,
 heterogeneous=heterogeneous,