From 5e2a87b5e6fc8b2d60dc0bcf19efd765bd86fcf6 Mon Sep 17 00:00:00 2001 From: John Lees Date: Wed, 29 Jan 2025 11:38:25 +0000 Subject: [PATCH] Start fixing some of the tests --- PopPUNK/network.py | 2 +- test/run_test.py | 7 ++++--- test/test-update.py | 8 ++++---- 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/PopPUNK/network.py b/PopPUNK/network.py index 6e9b4d7a..11fe3fc7 100644 --- a/PopPUNK/network.py +++ b/PopPUNK/network.py @@ -279,7 +279,7 @@ def translate_network_indices(G_ref_df, reference_indices): G_ref = generate_cugraph(G_ref_df, len(reference_indices) - 1, renumber = True) return(G_ref) -def extractReferences(G, dbOrder, outPrefix, merged_queries, outSuffix = '', type_isolate = None, +def extractReferences(G, dbOrder, outPrefix, merged_queries = list(), outSuffix = '', type_isolate = None, existingRefs = None, threads = 1, use_gpu = False, fast_mode = False): """Extract references for each cluster based on cliques diff --git a/test/run_test.py b/test/run_test.py index 2b8eb42c..858dee87 100755 --- a/test/run_test.py +++ b/test/run_test.py @@ -75,9 +75,10 @@ subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-pi-dist 0.04 --max-zero-dist 1 --betweenness --overwrite", shell=True, check=True) subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query more_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-zero-dist 0.3 --overwrite", shell=True, check=True) subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query more_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-zero-dist 1 --max-merge 3 --overwrite", shell=True, check=True) -subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update --update-db --graph-weights --overwrite", shell=True, check=True) # uses graph weights -subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query even_more_queries.txt --db example_query_update --model-dir example_dbscan --previous-clustering example_query_update --output example_query_update_2 --update-db --graph-weights --overwrite", shell=True, check=True) # uses graph weights -subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query single_query.txt --db example_db --model-dir example_refine --output example_single_query --update-db --overwrite", shell=True, check=True) +subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update --update-db full --graph-weights --overwrite", shell=True, check=True) # uses graph weights +subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update_fast --update-db fast --graph-weights --overwrite", shell=True, check=True) # uses graph weights +subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query even_more_queries.txt --db example_query_update --model-dir example_dbscan --previous-clustering example_query_update --output example_query_update_2 --update-db full --graph-weights --overwrite", shell=True, check=True) # uses graph weights +subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query single_query.txt --db example_db --model-dir example_refine --output example_single_query --update-db full --overwrite", shell=True, check=True) subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query inref_query.txt --db example_db --model-dir example_refine --output example_single_query --write-references", shell=True, check=True) # matched name, but should be renamed in the output subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_refine --model-dir example_lineages --output example_lineage_query --overwrite", shell=True, check=True) diff --git a/test/test-update.py b/test/test-update.py index e5870ac1..b2c41813 100755 --- a/test/test-update.py +++ b/test/test-update.py @@ -76,8 +76,8 @@ def old_get_seq_tuples(rows,cols): subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile1.txt --output batch1 --overwrite", shell=True, check=True) subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True) print("../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite\n\n") - subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1", shell=True, check=True) - print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1\n\n") + subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db full --overwrite --max-a-dist 1", shell=True, check=True) + print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db full --overwrite --max-a-dist 1\n\n") # Load updated distance order with open("batch2/batch2.dists.pkl", 'rb') as pickle_file: @@ -103,8 +103,8 @@ def old_get_seq_tuples(rows,cols): subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile123.txt --output batch123 --overwrite", shell=True, check=True) subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True) print("../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite\n\n") - subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite", shell=True, check=True) - print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite\n\n") + subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db full --overwrite", shell=True, check=True) + print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db full --overwrite\n\n") # Load updated distances order with open("batch3/batch3.dists.pkl", 'rb') as pickle_file: