Update beebop tests

bacpop · Oct 9, 2024 · 7982406 · 7982406
1 parent 395c2b9
commit 7982406
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Showing 4 changed files with 42 additions and 12 deletions.
diff --git a/test/batch12_external_clusters.csv b/test/batch12_external_clusters.csv
@@ -0,0 +1,18 @@
+Taxon,Cluster
+19183_4#67,CLUSTER1
+12754_5#55,CLUSTER1
+12754_5#57,CLUSTER1
+12673_8#34,CLUSTER1
+12754_5#71,CLUSTER1
+19183_4#69,CLUSTER1
+12754_4#85,CLUSTER1
+19183_4#66,CLUSTER1
+12754_4#89,CLUSTER2
+19183_4#55,CLUSTER2
+12754_5#73,CLUSTER3
+12754_4#79,CLUSTER3
+19183_4#63,CLUSTER4
+19183_4#59,CLUSTER5
+19183_4#48,CLUSTER6
+12754_5#37,CLUSTER7
+12754_4#71,CLUSTER8
diff --git a/test/rfile12.txt b/test/rfile12.txt
@@ -1,6 +1,17 @@
-7	12673_8#24.contigs_velvet.fa
-1	12673_8#34.contigs_velvet.fa
-2	12673_8#43.contigs_velvet.fa
-6	12754_4#79.contigs_velvet.fa
-4	12754_4#85.contigs_velvet.fa
-5	12754_4#89.contigs_velvet.fa
+12754_5#73	12754_5#73.contigs_velvet.fa
+12754_4#79	12754_4#79.contigs_velvet.fa
+12754_4#71	12754_4#71.contigs_velvet.fa
+19183_4#55	19183_4#55.contigs_velvet.fa
+19183_4#59	19183_4#59.contigs_velvet.fa
+12754_4#89	12754_4#89.contigs_velvet.fa
+19183_4#48	19183_4#48.contigs_velvet.fa
+12754_5#37	12754_5#37.contigs_velvet.fa
+19183_4#63	19183_4#63.contigs_velvet.fa
+12754_5#71	12754_5#71.contigs_velvet.fa
+19183_4#67	19183_4#67.contigs_velvet.fa
+19183_4#69	19183_4#69.contigs_velvet.fa
+12754_5#55	12754_5#55.contigs_velvet.fa
+12754_4#85	12754_4#85.contigs_velvet.fa
+12673_8#34	12673_8#34.contigs_velvet.fa
+19183_4#66	19183_4#66.contigs_velvet.fa
+12754_5#57	12754_5#57.contigs_velvet.fa
diff --git a/test/rfile3.txt b/test/rfile3.txt
@@ -1,3 +1,4 @@
-8	12754_5#73.contigs_velvet.fa
-3	12754_5#78.contigs_velvet.fa
-9	12754_5#71.contigs_velvet.fa
+12754_5#71	12754_5#71.contigs_velvet.fa
+12754_5#55	12754_5#55.contigs_velvet.fa
+12754_5#16	12754_5#16.contigs_velvet.fa
+12754_5#88	12754_5#88.contigs_velvet.fa
diff --git a/test/run_test.py b/test/run_test.py
@@ -126,9 +126,9 @@
     sys.exit(1)
 
 # beebop test
-subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile12.txt --output batch12 --overwrite", shell=True, check=True)
-subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model bgmm --D 2 --ref-db 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  --overwrite", shell=True, check=True)
+subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile12.txt  --min-k 13 --k-step 3 --output batch12 --overwrite", shell=True, check=True)
+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 --network-file ./batch12/batch12_graph.gt --overwrite", shell=True, check=True)