From 7982406db7f6e6dd56cdab1e84c24c5dbcc6bb69 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Wed, 9 Oct 2024 21:51:43 +0100 Subject: [PATCH] Update beebop tests --- test/batch12_external_clusters.csv | 18 ++++++++++++++++++ test/rfile12.txt | 23 +++++++++++++++++------ test/rfile3.txt | 7 ++++--- test/run_test.py | 6 +++--- 4 files changed, 42 insertions(+), 12 deletions(-) create mode 100644 test/batch12_external_clusters.csv diff --git a/test/batch12_external_clusters.csv b/test/batch12_external_clusters.csv new file mode 100644 index 00000000..01b480b3 --- /dev/null +++ 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 index e4f63584..51f99d88 100644 --- 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 index 23104358..2a5f859d 100644 --- 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 index 6379acae..fe496b74 100755 --- 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)