GIT: Merge changes from main

tests/test_cli_metacoag.py

@@ -1,18 +1,19 @@
+import os
 import pathlib
-import pytest
 
+import pytest
 from click.testing import CliRunner
 
 from gbintk.cli import metacoag
 
-
 __author__ = "Vijini Mallawaarachchi"
 __credits__ = ["Vijini Mallawaarachchi"]
 
 
 DATADIR = pathlib.Path(__file__).parent / "data"
 
-@pytest.fixture(scope="session")
+
+@pytest.fixture(scope="function")
 def tmp_dir(tmpdir_factory):
     return tmpdir_factory.mktemp("tmp")
 
@@ -29,12 +30,158 @@ def runner():
     return CliRunner()
 
 
-def test_metacoag_run(runner, tmp_dir):
+def get_files_and_seq_counts(output_path):
+    output_files = os.listdir(output_path)
+    seq_counts = []
+    for file in output_files:
+        seq_count = 0
+        with open(f"{output_path}/{file}", "r") as myfile:
+            for line in myfile:
+                if line.strip().startswith(">"):
+                    seq_count += 1
+        seq_counts.append(seq_count)
+
+    seq_counts.sort()
+
+    return len(output_files), seq_counts
+
+
+@pytest.fixture(scope="function")
+def test_metacoag_spades_run(runner, tmp_dir):
     outpath = tmp_dir
     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  # Check if the command ran successfully
+
+    n_bins, seq_counts = get_files_and_seq_counts(outpath / "bins")
+    return n_bins, seq_counts
+
+
+@pytest.fixture(scope="function")
+def test_metacoag_megahit_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "5G_MEGAHIT" / "final.gfa"
+    contigs = DATADIR / "5G_MEGAHIT" / "final.contigs.fa"
+    abundance = DATADIR / "5G_MEGAHIT" / "abundance.tsv"
+    args = f"--assembler megahit --graph {graph} --contigs {contigs} --abundance {abundance} --output {outpath}".split()
+    r = runner.invoke(metacoag, args, catch_exceptions=False)
+
+    assert r.exit_code == 0, r.output
+
+    n_bins, seq_counts = get_files_and_seq_counts(outpath / "bins")
+    return n_bins, seq_counts
+
+
+@pytest.fixture(scope="function")
+def test_metacoag_flye_run(tmp_dir, runner):
+    outpath = tmp_dir
+    graph = DATADIR / "1Y3B_Flye" / "assembly_graph.gfa"
+    contigs = DATADIR / "1Y3B_Flye" / "assembly.fasta"
+    paths = DATADIR / "1Y3B_Flye" / "assembly_info.txt"
+    abundance = DATADIR / "1Y3B_Flye" / "abundance.tsv"
+    args = f"--assembler flye --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
+
+    n_bins, seq_counts = get_files_and_seq_counts(outpath / "bins")
+    return n_bins, seq_counts
+
+
+def test_n_bins_metacoag_spades(test_metacoag_spades_run):
+    n_bins, seq_counts = test_metacoag_spades_run
+
+    # Assert number of bins
+    assert n_bins == 5
+
+    # Assert bin sizes
+    assert seq_counts == [10, 23, 48, 69, 78]
+
+
+@pytest.mark.filterwarnings("ignore::RuntimeWarning")
+def test_n_bins_metacoag_megahit(test_metacoag_megahit_run):
+    n_bins, seq_counts = test_metacoag_megahit_run
+
+    # Assert number of bins
+    assert n_bins == 5
+
+    # Assert bin sizes
+    assert seq_counts == [36, 40, 46, 84, 127]
+
+
+@pytest.mark.filterwarnings("ignore::RuntimeWarning")
+def test_n_bins_metacoag_flye(test_metacoag_flye_run):
+    n_bins, seq_counts = test_metacoag_flye_run
+
+    # Assert number of bins
+    assert n_bins == 3
+
+    # Assert bin sizes
+    assert seq_counts == [1, 1, 1]
+
+
+@pytest.mark.parametrize(
+    "graph, contigs, paths, abundance",
+    [
+        (
+            DATADIR / "invlid_path" / "assembly_graph_with_scaffolds.gfa",
+            DATADIR / "5G_metaSPAdes" / "contigs.fasta",
+            DATADIR / "5G_metaSPAdes" / "contigs.paths",
+            DATADIR / "5G_metaSPAdes" / "coverm_mean_coverage.tsv",
+        ),
+    ],
+)
+def test_metacoag_spades_invalid_run(runner, tmp_dir, graph, contigs, paths, abundance):
+    outpath = tmp_dir
+    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
+    assert "Error" in r.output and "Path" in r.output  # Check for error messages
+
+
+@pytest.mark.parametrize(
+    "graph, contigs, abundance",
+    [
+        (
+            DATADIR / "invalid_path" / "final.gfa",
+            DATADIR / "5G_MEGAHIT" / "final.contigs.fa",
+            DATADIR / "5G_MEGAHIT" / "abundance.tsv",
+        ),
+    ],
+)
+def test_metacoag_megahit_invalid_run(
+    runner, tmp_path_factory, graph, contigs, abundance
+):
+    outpath = tmp_path_factory.mktemp("tmp")
+    args = f"--assembler megahit --graph {graph} --contigs {contigs} --abundance {abundance} --output {outpath}".split()
+    r = runner.invoke(metacoag, args, catch_exceptions=True)
+
+    assert r.exit_code != 0
+    assert "Error" in r.output and "Path" in r.output
+
+
+@pytest.mark.parametrize(
+    "graph, contigs, paths, abundance",
+    [
+        (
+            DATADIR / "invalid_path" / "assembly_graph.gfa",
+            DATADIR / "1Y3B_Flye" / "assembly.fasta",
+            DATADIR / "1Y3B_Flye" / "assembly_info.txt",
+            DATADIR / "1Y3B_Flye" / "abundance.tsv",
+        ),
+    ],
+)
+def test_metacoag_flye_invalid_run(
+    runner, tmp_path_factory, graph, contigs, paths, abundance
+):
+    outpath = tmp_path_factory.mktemp("tmp")
+    args = f"--assembler flye --graph {graph} --contigs {contigs} --paths {paths} --abundance {abundance} --output {outpath}".split()
+    r = runner.invoke(metacoag, args, catch_exceptions=True)
+
+    assert r.exit_code != 0
+    assert "Error" in r.output and "Path" in r.output