TST: Update tests to check bins

tests/test_metacoag.py

@@ -1,3 +1,4 @@
+import os
 import subprocess
 from pathlib import Path
 
@@ -9,24 +10,13 @@
 __version__ = "1.1.1"
 __maintainer__ = "Vijini Mallawaarachchi"
 __email__ = "vijini.mallawaarachchi@anu.edu.au"
-__status__ = "Development"
+__status__ = "Stable Release"
 
 
 TEST_ROOTDIR = Path(__file__).parent
 EXEC_ROOTDIR = Path(__file__).parent.parent
 
 
-@pytest.fixture(scope="session")
-def tmp_dir(tmpdir_factory):
-    return tmpdir_factory.mktemp("tmp")
-
-
-@pytest.fixture(autouse=True)
-def workingdir(tmp_dir, monkeypatch):
-    """set the working directory for all tests"""
-    monkeypatch.chdir(tmp_dir)
-
-
 def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
     """executes shell command and returns stdout if completes exit code 0
     Parameters
@@ -44,8 +34,28 @@ def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
     return out.decode("utf8") if out is not None else None
 
 
-def test_metacoag_spades_command(tmp_dir):
-    """test metacoag on spades assembly"""
+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="session")
+def test_metacoag_spades_command(tmp_path_factory):
+    """test metacoag on metaspades assembly"""
+
+    tmp_dir = tmp_path_factory.mktemp("tmp")
+
     dir_name = TEST_ROOTDIR / "data" / "5G_metaspades"
     graph = dir_name / "assembly_graph_with_scaffolds.gfa"
     contigs = dir_name / "contigs.fasta"
@@ -54,12 +64,46 @@ def test_metacoag_spades_command(tmp_dir):
     cmd = f"metacoag --assembler spades --graph {graph} --contigs {contigs} --paths {paths} --abundance {abundance} --output {tmp_dir}"
     exec_command(cmd)
 
+    n_bins, seq_counts = get_files_and_seq_counts(tmp_dir / "bins")
+
+    return n_bins, seq_counts
+
+
+def test_n_bins_metacoag_spades(test_metacoag_spades_command):
+    n_bins, seq_counts = test_metacoag_spades_command
 
-def test_metacoag_megahit_command(tmp_dir):
+    # Assert number of bins
+    assert n_bins == 5
+
+    # Assert bin sizes
+    assert seq_counts == [10, 23, 48, 69, 78]
+
+
+@pytest.fixture(scope="session")
+def test_metacoag_megahit_command(tmp_path_factory):
     """test metacoag on megahit assembly"""
+
+    tmp_dir = tmp_path_factory.mktemp("tmp")
+
     dir_name = TEST_ROOTDIR / "data" / "5G_MEGAHIT"
     graph = dir_name / "final.gfa"
     contigs = dir_name / "final.contigs.fa"
     abundance = dir_name / "abundance.tsv"
     cmd = f"metacoag --assembler megahit --graph {graph} --contigs {contigs} --abundance {abundance} --output {tmp_dir}"
     exec_command(cmd)
+
+    n_bins, seq_counts = get_files_and_seq_counts(tmp_dir / "bins")
+
+    return n_bins, seq_counts
+
+
+def test_n_bins_metacoag_megahit(test_metacoag_megahit_command):
+    n_bins, seq_counts = test_metacoag_megahit_command
+
+    # Assert number of bins
+    assert n_bins == 5
+
+    # Assert bin sizes
+    assert seq_counts == [36, 40, 46, 84, 127]
+
+