TST: Update test data and test cases

metagentools · Aug 13, 2024 · a148a7b · a148a7b
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Showing 17 changed files with 29 additions and 142,660 deletions.
diff --git a/tests/data/Sim-5G+metaSPAdes/abundance.abund → tests/data/5G_metaSPAdes/abundance.abund b/tests/data/Sim-5G+metaSPAdes/abundance.abund → tests/data/5G_metaSPAdes/abundance.abund
diff --git a/...aSPAdes/assembly_graph_with_scaffolds.gfa → ...aSPAdes/assembly_graph_with_scaffolds.gfa b/...aSPAdes/assembly_graph_with_scaffolds.gfa → ...aSPAdes/assembly_graph_with_scaffolds.gfa
diff --git a/tests/data/Sim-5G+metaSPAdes/contigs.fasta → tests/data/5G_metaSPAdes/contigs.fasta b/tests/data/Sim-5G+metaSPAdes/contigs.fasta → tests/data/5G_metaSPAdes/contigs.fasta
diff --git a/...ta/Sim-5G+metaSPAdes/contigs.fasta.hmmout → ...s/data/5G_metaSPAdes/contigs.fasta.hmmout b/...ta/Sim-5G+metaSPAdes/contigs.fasta.hmmout → ...s/data/5G_metaSPAdes/contigs.fasta.hmmout
diff --git a/tests/data/Sim-5G+metaSPAdes/contigs.paths → tests/data/5G_metaSPAdes/contigs.paths b/tests/data/Sim-5G+metaSPAdes/contigs.paths → tests/data/5G_metaSPAdes/contigs.paths
diff --git a/...im-5G+metaSPAdes/coverm_mean_coverage.tsv → ...ta/5G_metaSPAdes/coverm_mean_coverage.tsv b/...im-5G+metaSPAdes/coverm_mean_coverage.tsv → ...ta/5G_metaSPAdes/coverm_mean_coverage.tsv
diff --git a/...s/data/Sim-5G+metaSPAdes/graphbin_res.csv → tests/data/5G_metaSPAdes/graphbin_res.csv b/...s/data/Sim-5G+metaSPAdes/graphbin_res.csv → tests/data/5G_metaSPAdes/graphbin_res.csv
diff --git a/...Sim-5G+metaSPAdes/initial_contig_bins.csv → ...ata/5G_metaSPAdes/initial_contig_bins.csv b/...Sim-5G+metaSPAdes/initial_contig_bins.csv → ...ata/5G_metaSPAdes/initial_contig_bins.csv
diff --git a/...s/data/Sim-5G+metaSPAdes/metacoag_res.csv → tests/data/5G_metaSPAdes/metacoag_res.csv b/...s/data/Sim-5G+metaSPAdes/metacoag_res.csv → tests/data/5G_metaSPAdes/metacoag_res.csv
diff --git a/tests/data/ESC_metaSPAdes/assembly_graph_with_scaffolds.gfa b/tests/data/ESC_metaSPAdes/assembly_graph_with_scaffolds.gfa
diff --git a/tests/data/ESC_metaSPAdes/contigs.fasta b/tests/data/ESC_metaSPAdes/contigs.fasta
diff --git a/tests/data/ESC_metaSPAdes/contigs.paths b/tests/data/ESC_metaSPAdes/contigs.paths
diff --git a/tests/data/ESC_metaSPAdes/initial_binning_res.csv b/tests/data/ESC_metaSPAdes/initial_binning_res.csv
diff --git a/tests/test_cli_graphbin.py b/tests/test_cli_graphbin.py
@@ -31,10 +31,10 @@ def runner():
 
 def test_graphbin_run(runner, tmp_dir):
     outpath = tmp_dir
-    graph = DATADIR / "ESC_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "ESC_metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "ESC_metaSPAdes" / "contigs.paths"
-    binned = DATADIR / "ESC_metaSPAdes" / "initial_binning_res.csv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "5G_metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
+    binned = DATADIR / "5G_metaSPAdes" / "initial_contig_bins.csv"
     args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --output {outpath}".split()
     r = runner.invoke(graphbin, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output
diff --git a/tests/test_cli_graphbin2.py b/tests/test_cli_graphbin2.py
@@ -31,11 +31,11 @@ def runner():
 
 def test_graphbin2_run(runner, tmp_dir):
     outpath = tmp_dir
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
-    binned = DATADIR / "Sim-5G+metaSPAdes" / "initial_contig_bins.csv"
-    abundance = DATADIR / "Sim-5G+metaSPAdes" / "abundance.abund"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "5G_metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
+    binned = DATADIR / "5G_metaSPAdes" / "initial_contig_bins.csv"
+    abundance = DATADIR / "5G_metaSPAdes" / "abundance.abund"
     args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --abundance {abundance} --output {outpath}".split()
     r = runner.invoke(graphbin2, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output

diff --git a/tests/test_cli_metacoag.py b/tests/test_cli_metacoag.py
@@ -31,10 +31,10 @@ def runner():
 
 def test_metacoag_run(runner, tmp_dir):
     outpath = tmp_dir
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
-    abundance = DATADIR / "Sim-5G+metaSPAdes" / "coverm_mean_coverage.tsv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "5G_metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
+    abundance = DATADIR / "5G_metaSPAdes" / "coverm_mean_coverage.tsv"
     args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --abundance {abundance} --output {outpath}".split()
     r = runner.invoke(metacoag, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output
diff --git a/tests/test_visualise.py b/tests/test_visualise.py
@@ -31,40 +31,40 @@ def runner():
 
 def test_visualise_run(runner, tmp_dir):
     outpath = tmp_dir
-    initial = DATADIR / "Sim-5G+metaSPAdes" / "metacoag_res.csv"
-    final = DATADIR / "Sim-5G+metaSPAdes" / "graphbin_res.csv"
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    initial = DATADIR / "5G_metaSPAdes" / "metacoag_res.csv"
+    final = DATADIR / "5G_metaSPAdes" / "graphbin_res.csv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
     args = f"--assembler spades --initial {initial} --final {final} --graph {graph} --paths {paths} --output {outpath}".split()
     r = runner.invoke(visualise, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output
 
 def test_visualise_prefix(runner, tmp_dir):
     outpath = tmp_dir
-    initial = DATADIR / "Sim-5G+metaSPAdes" / "metacoag_res.csv"
-    final = DATADIR / "Sim-5G+metaSPAdes" / "graphbin_res.csv"
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    initial = DATADIR / "5G_metaSPAdes" / "metacoag_res.csv"
+    final = DATADIR / "5G_metaSPAdes" / "graphbin_res.csv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
     args = f"--assembler spades --initial {initial} --final {final} --graph {graph} --paths {paths} --prefix test --output {outpath}".split()
     r = runner.invoke(visualise, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output
 
 def test_visualise_imgtype(runner, tmp_dir):
     outpath = tmp_dir
-    initial = DATADIR / "Sim-5G+metaSPAdes" / "metacoag_res.csv"
-    final = DATADIR / "Sim-5G+metaSPAdes" / "graphbin_res.csv"
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    initial = DATADIR / "5G_metaSPAdes" / "metacoag_res.csv"
+    final = DATADIR / "5G_metaSPAdes" / "graphbin_res.csv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
     args = f"--assembler spades --initial {initial} --final {final} --graph {graph} --paths {paths} --imgtype svg --output {outpath}".split()
     r = runner.invoke(visualise, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output
 
 def test_visualise_outdir(runner, tmp_dir):
     outpath = tmp_dir / "testing"
-    initial = DATADIR / "Sim-5G+metaSPAdes" / "metacoag_res.csv"
-    final = DATADIR / "Sim-5G+metaSPAdes" / "graphbin_res.csv"
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    initial = DATADIR / "5G_metaSPAdes" / "metacoag_res.csv"
+    final = DATADIR / "5G_metaSPAdes" / "graphbin_res.csv"
+    graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    paths = DATADIR / "5G_metaSPAdes" / "contigs.paths"
     args = f"--assembler spades --initial {initial} --final {final} --graph {graph} --paths {paths} --output {outpath}".split()
     r = runner.invoke(visualise, args, catch_exceptions=False)
     assert r.exit_code == 0, r.output