Merge pull request #37 from iqbal-lab-org/fix/add_integration_tests_t…

…o_all_pling_commands

Plasnet integration PR series (5/5): tests: add integration tests to all pling commands

.github/workflows/ci.yaml

@@ -4,16 +4,18 @@ on:
   push:
     branches:
       - main
+      - dev
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   Testing:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ ubuntu-latest, macos-latest ]
+        os: [ ubuntu-latest ]
         python-version: [ 3.8, 3.9, "3.10", 3.11 ]
     steps:
       - uses: actions/checkout@v3
@@ -30,11 +32,23 @@ jobs:
             python=${{ matrix.python-version }}
             snakemake
             mamba
+            poetry
           init-shell: bash
           cache-environment: true
           post-cleanup: 'all'
-      - name: Test workflow (local test data)
+
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Install
+        shell: bash -el {0}
+        run: |
+          micromamba activate test-env
+          make install-ci
+
+      - name: Test
         shell: bash -el {0}
         run: |
           micromamba activate test-env
-          python -m unittest discover -v -v -v -s tests -t .
+          make test

Makefile

@@ -0,0 +1,26 @@
+# Inspired by https://github.com/snakemake/snakefmt/blob/master/Makefile
+PROJECT = pling
+OS := $(shell uname -s)
+VERSION := $(shell poetry version -s)
+BOLD := $(shell tput bold)
+NORMAL := $(shell tput sgr0)
+
+.PHONY: all
+all: install
+
+.PHONY: install
+install:
+	poetry install
+
+.PHONY: install-ci
+install-ci:
+	poetry install --no-interaction
+	poetry run pling --help
+
+.PHONY: test
+test:
+	poetry run python -m unittest discover -s tests -t .
+
+.PHONY: build
+build:
+	poetry build

pyproject.toml

@@ -14,9 +14,9 @@ keywords = ["Plasmids", "Comparative genomics", "Genome rearrangement", "DCJ-ind
 pling = 'pling.run_pling:main'
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.13"
+python = ">=3.8,<3.13"
 snakemake = "^7.32.4"
-pandas = "^2.1.1"
+pandas = "^2.0.3"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

tests/integration_test/data/all_plasmids_distances.align.truth.tsv

@@ -0,0 +1,17 @@
+	plasmid_1	plasmid_2	distance
+0	CP057418.1	CP057418.1	0
+1	CP057418.1	NZ_CP027199.1	23
+2	CP057418.1	NZ_LR882977.1	19
+3	CP057418.1	NZ_MF510423.1	
+4	NZ_CP027199.1	CP057418.1	23
+5	NZ_CP027199.1	NZ_CP027199.1	0
+6	NZ_CP027199.1	NZ_LR882977.1	19
+7	NZ_CP027199.1	NZ_MF510423.1	
+8	NZ_LR882977.1	CP057418.1	19
+9	NZ_LR882977.1	NZ_CP027199.1	19
+10	NZ_LR882977.1	NZ_LR882977.1	0
+11	NZ_LR882977.1	NZ_MF510423.1	
+12	NZ_MF510423.1	CP057418.1	
+13	NZ_MF510423.1	NZ_CP027199.1	
+14	NZ_MF510423.1	NZ_LR882977.1	
+15	NZ_MF510423.1	NZ_MF510423.1	0

tests/integration_test/data/all_plasmids_distances.anno.truth.tsv

@@ -0,0 +1,17 @@
+	plasmid_1	plasmid_2	distance
+0	CP057418.1	CP057418.1	0
+1	CP057418.1	NZ_CP027199.1	18
+2	CP057418.1	NZ_LR882977.1	14
+3	CP057418.1	NZ_MF510423.1	
+4	NZ_CP027199.1	CP057418.1	18
+5	NZ_CP027199.1	NZ_CP027199.1	0
+6	NZ_CP027199.1	NZ_LR882977.1	16
+7	NZ_CP027199.1	NZ_MF510423.1	
+8	NZ_LR882977.1	CP057418.1	14
+9	NZ_LR882977.1	NZ_CP027199.1	16
+10	NZ_LR882977.1	NZ_LR882977.1	0
+11	NZ_LR882977.1	NZ_MF510423.1	
+12	NZ_MF510423.1	CP057418.1	
+13	NZ_MF510423.1	NZ_CP027199.1	
+14	NZ_MF510423.1	NZ_LR882977.1	
+15	NZ_MF510423.1	NZ_MF510423.1	0

tests/integration_test/data/all_plasmids_matrix.align.truth.dist

@@ -0,0 +1,5 @@
+4				
+CP057418.1	0	23	19	
+NZ_CP027199.1	23	0	19	
+NZ_LR882977.1	19	19	0	
+NZ_MF510423.1				0

tests/integration_test/data/all_plasmids_matrix.anno.truth.dist

@@ -0,0 +1,5 @@
+4				
+CP057418.1	0	18	14	
+NZ_CP027199.1	18	0	16	
+NZ_LR882977.1	14	16	0	
+NZ_MF510423.1				0

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab

@@ -0,0 +1,2 @@
+#taxgroup	accession_version	mutation_position	mutation_symbol	class	subclass	mutated_protein_name
+Escherichia	WP_000019358.1	12	soxS_A12S	MULTIDRUG	AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE	Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress

@@ -0,0 +1,2 @@
+#taxgroup	protein_accession	protein_gi
+Escherichia	AAA21095.1	151858

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab

@@ -0,0 +1,2 @@
+#taxgroup	gene_symbol	accession_version	resistance_cutoff	class	subclass	resistance_protein_name
+Streptococcus_pneumoniae	pbp1a	WP_001040013.1	           99.000000	BETA-LACTAM	BETA-LACTAM	Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/database_format_version.txt

@@ -0,0 +1 @@
+3.10.16

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/taxgroup.tab

@@ -0,0 +1,2 @@
+#taxgroup	gpipe_taxgroup	number_of_nucl_ref_genes
+Acinetobacter_baumannii	Acinetobacter	0

tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/version.txt

@@ -0,0 +1 @@
+2021-09-30.1

tests/integration_test/data/bakta_db/amrfinderplus-db/latest

@@ -0,0 +1 @@
+2021-09-30.1

tests/integration_test/data/bakta_db/oric.fna

@@ -0,0 +1,4 @@
+>ORI10010001
+TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA
+>ORI10010003
+GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT

tests/integration_test/data/bakta_db/orit.fna

@@ -0,0 +1,4 @@
+>CP019995|MOBP
+GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC
+>CP012386|MOBP
+AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA

tests/integration_test/data/bakta_db/rfam-go.tsv

@@ -0,0 +1 @@
+Rfam:RF00001	GO:0003735

tests/integration_test/data/bakta_db/version.json

@@ -0,0 +1,54 @@
+{
+  "date": "2023-02-20",
+  "major": 5,
+  "minor": 0,
+  "type": "full",
+  "dependencies": [
+    {
+      "name": "AMRFinderPlus",
+      "release": "2020-09-22.2"
+    },
+    {
+      "name": "COG",
+      "release": "2014"
+    },
+    {
+      "name": "DoriC",
+      "release": "10"
+    },
+    {
+      "name": "ISFinder",
+      "release": "2019-09-25"
+    },
+    {
+      "name": "Mob-suite",
+      "release": "2.0"
+    },
+    {
+      "name": "Pfam",
+      "release": "33.1"
+    },
+    {
+      "name": "RefSeq",
+      "release": "r202"
+    },
+    {
+      "name": "Rfam",
+      "release": "14.2"
+    },
+    {
+      "name": "UniProtKB/Swiss-Prot",
+      "release": "2020_04"
+    }
+  ],
+  "experts": [
+    {
+      "name": "AMRFinderPlus",
+      "release": "3.10.1"
+    },
+    {
+      "name": "NCBI BlastRules",
+      "release": "4.0"
+    }
+  ]
+}

tests/integration_test/test_integration_test.py

@@ -15,12 +15,12 @@ def assert_files_are_identical(self, path_to_first_file, path_to_second_file):
         second_file_content = self.read_file(path_to_second_file)
         self.assertEqual(first_file_content, second_file_content)
 
-    def test_pling_end_to_end(self):
+    def test_pling_align_end_to_end(self):
         args = Namespace(genomes_list='tests/integration_test/data/incy_list_4.txt',
-                         output_dir='tests/integration_test/data/out',
+                         output_dir='tests/integration_test/data/out_align',
                          integerisation='align',
                          bakta_db=None,
-                         jaccard=0.4,
+                         jaccard_distance=0.6,
                          dcj=4,
                          dedup=None,
                          dedup_threshold=None,
@@ -38,5 +38,63 @@ def test_pling_end_to_end(self):
                          profile=None)
         run_pling.pling(args)
 
-        assert_files_are_identical("tests/integration_test/data/out/all_plasmids_matrix.dist",
-                                   "tests/integration_test/data/all_plasmids_matrix.truth.dist")
+        assert_files_are_identical("tests/integration_test/data/out_align/all_plasmids_matrix.dist",
+                                   "tests/integration_test/data/all_plasmids_matrix.align.truth.dist")
+        assert_files_are_identical("tests/integration_test/data/out_align/all_plasmids_distances.tsv",
+                                   "tests/integration_test/data/all_plasmids_distances.align.truth.tsv")
+
+    def test_pling_anno_with_dedup_end_to_end(self):
+        args = Namespace(genomes_list='tests/integration_test/data/incy_list_4.txt',
+                         output_dir='tests/integration_test/data/out_anno_with_dedup',
+                         integerisation='anno',
+                         bakta_db="tests/integration_test/data/bakta_db",
+                         jaccard_distance=0.6,
+                         dcj=4,
+                         dedup=True,
+                         dedup_threshold=98.5,
+                         identity=80,
+                         min_indel_size=200,
+                         bh_connectivity=10,
+                         bh_neighbours_edge_density=0.2,
+                         small_subcommunity_size_threshold=4,
+                         cores='2',
+                         storetmp=False,
+                         forceall=True,
+                         ilp_solver='GLPK',
+                         timelimit=None,
+                         resources=None,
+                         profile=None)
+        run_pling.pling(args)
+
+        assert_files_are_identical("tests/integration_test/data/out_anno_with_dedup/all_plasmids_matrix.dist",
+                                   "tests/integration_test/data/all_plasmids_matrix.anno.truth.dist")
+        assert_files_are_identical("tests/integration_test/data/out_anno_with_dedup/all_plasmids_distances.tsv",
+                                   "tests/integration_test/data/all_plasmids_distances.anno.truth.tsv")
+
+    def test_pling_anno_without_dedup_end_to_end(self):
+        args = Namespace(genomes_list='tests/integration_test/data/incy_list_4.txt',
+                         output_dir='tests/integration_test/data/out_anno_without_dedup',
+                         integerisation='anno',
+                         bakta_db="tests/integration_test/data/bakta_db",
+                         jaccard_distance=0.6,
+                         dcj=4,
+                         dedup=None,
+                         dedup_threshold=None,
+                         identity=80,
+                         min_indel_size=200,
+                         bh_connectivity=10,
+                         bh_neighbours_edge_density=0.2,
+                         small_subcommunity_size_threshold=4,
+                         cores='2',
+                         storetmp=False,
+                         forceall=True,
+                         ilp_solver='GLPK',
+                         timelimit=None,
+                         resources=None,
+                         profile=None)
+        run_pling.pling(args)
+
+        assert_files_are_identical("tests/integration_test/data/out_anno_without_dedup/all_plasmids_matrix.dist",
+                                   "tests/integration_test/data/all_plasmids_matrix.anno.truth.dist")
+        assert_files_are_identical("tests/integration_test/data/out_anno_without_dedup/all_plasmids_distances.tsv",
+                                   "tests/integration_test/data/all_plasmids_distances.anno.truth.tsv")