Add incomplete epi info to microreact

bacpop · Dec 9, 2024 · 78ee2e3 · 78ee2e3
1 parent a5e69b1
commit 78ee2e3
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Showing 3 changed files with 13 additions and 9 deletions.
diff --git a/PopPUNK/plot.py b/PopPUNK/plot.py
@@ -730,14 +730,13 @@ def writeClusterCsv(outfile, nodeNames, nodeLabels, clustering,
                         d['Status'].append("Reference")
             if epiCsv is not None:
                 if label in epiData.index:
-                    if label in epiData.index:
-                        for col, value in zip(epiData.columns.values, epiData.loc[[label]].iloc[0].values):
-                            if col not in columns_to_be_omitted:
-                                d[col].append(str(value))
-                    else:
-                        for col in epiData.columns.values:
-                            if col not in columns_to_be_omitted:
-                                d[col].append('nan')
+                    for col, value in zip(epiData.columns.values, epiData.loc[[label]].iloc[0].values):
+                        if col not in columns_to_be_omitted:
+                            d[col].append(str(value))
+                else:
+                    for col in epiData.columns.values:
+                        if col not in columns_to_be_omitted:
+                            d[col].append('')
 
         else:
             sys.stderr.write("Cannot find " + name + " in clustering\n")

diff --git a/test/batch123_info.csv b/test/batch123_info.csv
@@ -0,0 +1,5 @@
+id,Location
+19183_4#55,CountryX
+19183_4#48,CountryY
+12754_4#89,CountryZ
+12754_5#16,CountryZ
diff --git a/test/run_test.py b/test/run_test.py
@@ -134,7 +134,7 @@
 subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model dbscan --ref-db batch12 --output batch12 --overwrite", shell=True, check=True)
 subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model refine --ref-db batch12 --output batch12 --overwrite", shell=True, check=True)
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch12 --query rfile3.txt --output batch3 --external-clustering batch12_external_clusters.csv --save-partial-query-graph  --overwrite", shell=True, check=True)
-subprocess.run(python_cmd + " ../poppunk_visualise-runner.py --ref-db batch12 --query-db batch3 --output batch123_viz --external-clustering batch12_external_clusters.csv --previous-query-clustering batch3/batch3_external_clusters.csv --cytoscape --rapidnj rapidnj --use-partial-query-graph ./batch3/batch3_query.subset --recalculate-distances --extend-query-graph --overwrite", shell=True, check=True)
+subprocess.run(python_cmd + " ../poppunk_visualise-runner.py --ref-db batch12 --query-db batch3 --output batch123_viz --external-clustering batch12_external_clusters.csv --previous-query-clustering batch3/batch3_external_clusters.csv --cytoscape --rapidnj rapidnj --use-partial-query-graph ./batch3/batch3_query.subset --recalculate-distances --extend-query-graph --info-csv batch123_info.csv --microreact --overwrite", shell=True, check=True)
 
 # citations
 sys.stderr.write("Printing citations\n")