update tests

tests/cds_test.py

@@ -118,14 +118,14 @@ def test_write_faa(contig1, orf_finder):
 
     predicted_genes = orf_finder.find_genes(contig1.seq)
     contig_name = "contig"
-    output_file = "tests/tmp_file.faa"
+    output_file = "tests/tmp_file.faa.gz"
 
     cds.write_faa(output_file, [(contig_name, predicted_genes)])
 
     # Check if the file was created and first seq starts
     # with the contig name as expected
     assert Path(output_file).exists()
-    with open(output_file, "r") as f:
+    with gzip.open(output_file, "rt") as f:
         assert f.read().startswith(f">{contig_name}")
 
 

tests/contig_manager_test.py

@@ -4,12 +4,13 @@
 
 
 # Parses a valid FASTA file and returns a pyfastx.Fasta object.
-def test_valid_fasta_file():
+def test_valid_fasta_file(tmp_path):
     # Arrange
     fasta_file = "tests/contigs.fasta"
 
-    # Act
-    result = contig_manager.parse_fasta_file(fasta_file)
+    index_file = "tests/contigs.fasta.fxi"
+
+    result = contig_manager.parse_fasta_file(fasta_file, str(index_file))
 
     # Assert
     assert isinstance(result, pyfastx.Fasta)
@@ -22,7 +23,7 @@ def test_invalid_fasta_file():
 
     # Act and Assert
     with pytest.raises(RuntimeError):
-        contig_manager.parse_fasta_file(fasta_file)
+        contig_manager.parse_fasta_file(fasta_file, "./index.fxi")
 
 
 # The function returns a tuple containing two dictionaries.

tests/diamonds_test.py

@@ -155,7 +155,7 @@ def __init__(self, returncode):
         # Simulating successful run of diamond command
         if (
             args[0]
-            == "diamond blastp --outfmt 6 --max-target-seqs 1 --query test.faa -o output.txt --threads 1 --db db --query-cover 80 --subject-cover 80 --id 30 --evalue 1e-05 --block-size 2 2> log.txt"
+            == "diamond blastp --outfmt 6 --max-target-seqs 1 --query test.faa -o output.txt --threads 1 --db db --compress 1 --query-cover 80 --subject-cover 80 --id 30 --evalue 1e-05 --block-size 2 2> log.txt"
         ):
             return CompletedProcess(0)
 

tests/main_binette_test.py

@@ -136,6 +136,7 @@ def test_manage_protein_alignement_resume(tmp_path):
         contig_to_kegg_counter, contig_to_genes = manage_protein_alignement(
             faa_file=Path(faa_file),
             contigs_fasta=Path("contigs_fasta"),
+            temporary_dir=Path(tmp_path),
             contig_to_length=contig_to_length,
             contigs_in_bins=set(),
             diamond_result_file=Path("diamond_result_file"),
@@ -179,6 +180,7 @@ def test_manage_protein_alignement_not_resume(tmpdir, tmp_path):
         contig_to_kegg_counter, contig_to_genes = manage_protein_alignement(
             faa_file=Path(faa_file),
             contigs_fasta=Path(contigs_fasta),
+            temporary_dir=Path(tmp_path),
             contig_to_length=contig_to_length,
             contigs_in_bins=set(),
             diamond_result_file=Path(diamond_result_file),
@@ -208,7 +210,7 @@ def test_parse_input_files_with_contig2bin_tables(tmp_path):
 
     # Call the function and capture the return values
     original_bins, contigs_in_bins, contig_to_length = parse_input_files(
-        None, [bin_set1, bin_set2], fasta_file
+        None, [bin_set1, bin_set2], fasta_file, tmp_path
     )
 
     # # Perform assertions on the returned values
@@ -230,7 +232,7 @@ def test_parse_input_files_with_contig2bin_tables_with_unknown_contig(tmp_path):
     fasta_file.write_text(fasta_file_content)
 
     with pytest.raises(ValueError):
-        parse_input_files(None, [bin_set3], fasta_file)
+        parse_input_files(None, [bin_set3], fasta_file, tmp_path)
 
 
 def test_parse_input_files_bin_dirs(create_temp_bin_directories, tmp_path):
@@ -247,7 +249,7 @@ def test_parse_input_files_bin_dirs(create_temp_bin_directories, tmp_path):
 
     # Call the function and capture the return values
     original_bins, contigs_in_bins, contig_to_length = parse_input_files(
-        bin_dirs, contig2bin_tables, fasta_file
+        bin_dirs, contig2bin_tables, fasta_file, temporary_dir=tmp_path
     )
 
     # # Perform assertions on the returned values
@@ -384,6 +386,7 @@ def test_manage_protein_alignment_no_resume(tmp_path):
         contig_to_kegg_counter, contig_to_genes = manage_protein_alignement(
             faa_file,
             contigs_fasta,
+            tmp_path,
             contig_to_length,
             contigs_in_bins,
             diamond_result_file,
@@ -395,7 +398,7 @@ def test_manage_protein_alignment_no_resume(tmp_path):
         )
 
         # Assertions to check if functions were called
-        mock_parse_fasta_file.assert_called_once_with(contigs_fasta.as_posix())
+        mock_parse_fasta_file.assert_called_once()
         mock_predict.assert_called_once()
         mock_diamond_get_contig_to_kegg_id.assert_called_once()
         mock_diamond_run.assert_called_once_with(