TST: add tests for graphbin, fixes #2

tests/test_cli_graphbin.py

@@ -12,6 +12,7 @@
 
 DATADIR = pathlib.Path(__file__).parent / "data"
 
+
 @pytest.fixture(scope="session")
 def tmp_dir(tmpdir_factory):
     return tmpdir_factory.mktemp("tmp")
@@ -29,7 +30,7 @@ def runner():
     return CliRunner()
 
 
-def test_graphbin_run(runner, tmp_dir):
+def test_graphbin_spades_run(runner, tmp_dir):
     outpath = tmp_dir
     graph = DATADIR / "5G_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
     contigs = DATADIR / "5G_metaSPAdes" / "contigs.fasta"
@@ -38,3 +39,24 @@ def test_graphbin_run(runner, tmp_dir):
     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
+
+
+def test_graphbin_megahit_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "5G_MEGAHIT" / "final.gfa"
+    contigs = DATADIR / "5G_MEGAHIT" / "final.contigs.fa"
+    binned = DATADIR / "5G_MEGAHIT" / "initial_contig_bins.csv"
+    args = f"--assembler megahit --graph {graph} --contigs {contigs} --binned {binned} --output {outpath}".split()
+    r = runner.invoke(graphbin, args, catch_exceptions=False)
+    assert r.exit_code == 0, r.output
+
+
+def test_graphbin_flye_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "1Y3B_Flye" / "assembly_graph.gfa"
+    contigs = DATADIR / "1Y3B_Flye" / "assembly.fasta"
+    paths = DATADIR / "1Y3B_Flye" / "assembly_info.txt"
+    binned = DATADIR / "1Y3B_Flye" / "initial_contig_bins.csv"
+    args = f"--assembler flye --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