feat: add debug flag to process_and_reroot_lineages function

barcodeforge/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.1.1"

barcodeforge/cli.py

@@ -236,6 +236,7 @@ def barcode(
     )
 
     process_and_reroot_lineages(
+        debug=is_debug,
         sample_muts_path=os.path.join(intermediate_dir, "samplePaths.txt"),
         reference_fasta_path=reference_genome,
         sequences_fasta_path=alignment,

barcodeforge/ref_muts.py

@@ -117,6 +117,7 @@ def _sanitize_mutation_data(mutations):
 
 
 def process_and_reroot_lineages(
+    debug: bool,
     sample_muts_path: str,
     reference_fasta_path: str,
     sequences_fasta_path: str,
@@ -146,6 +147,11 @@ def process_and_reroot_lineages(
         for i in additional_muts.keys():
             additional_muts[i]["ref"] = additional_muts[i].pop("base")
             additional_muts[i]["root"] = additional_muts[i].pop("mut")
+
+        if debug:
+            console.print(
+                f"[{STYLES['debug']}]Additional mutations derived from reference {ref.id}: {additional_muts}[/{STYLES['debug']}]"
+            )
     # else generate the root sequence
     else:
         console.print(

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "BarcodeForge"
-version = "1.0.0"
+version = "1.1.1"
 description = "A CLI tool for generating pathogen-specific barcodes for Freyja."
 readme = "README.md"
 requires-python = ">=3.10"

tests/test_cli.py

@@ -193,6 +193,7 @@ def test_barcode_command_default_options(runner, temp_files, mocker):
     mock_run_subp.assert_has_calls(expected_subprocess_calls, any_order=False)
 
     mock_process_reroot.assert_called_once_with(
+        debug=False,
         sample_muts_path=matutils_S_output_fn,
         reference_fasta_path=temp_files["ref_genome"],
         sequences_fasta_path=temp_files["alignment"],
@@ -207,9 +208,9 @@ def test_barcode_command_default_options(runner, temp_files, mocker):
         prefix="",  # Default prefix ""
     )
     mock_create_plot.assert_called_once_with(
-        debug=False,  # Add the debug argument
+        debug=False,
         input_file_path=final_barcodes_csv_fn,
-        chunk_size=100,  # Add chunk_size, default from CLI is 100
+        chunk_size=100,
         output_file_path=final_barcode_plot_fn,
     )
 
@@ -349,6 +350,7 @@ def test_barcode_command_custom_options(runner, temp_files, mocker):
     mock_run_subp.assert_has_calls(expected_subprocess_calls, any_order=False)
 
     mock_process_reroot.assert_called_once_with(
+        debug=False,
         sample_muts_path=matutils_S_output_fn,
         reference_fasta_path=temp_files["ref_genome"],
         sequences_fasta_path=temp_files["alignment"],
@@ -357,15 +359,15 @@ def test_barcode_command_custom_options(runner, temp_files, mocker):
         output_rerooted_lineage_paths_path=rerooted_lineage_paths_fn,
     )
     mock_create_barcodes.assert_called_once_with(
-        debug=False,  # Add the debug argument
+        debug=False,
         input_file_path=rerooted_lineage_paths_fn,
         output_file_path=final_barcodes_csv_fn,
         prefix=prefix,
     )
     mock_create_plot.assert_called_once_with(
-        debug=False,  # Add the debug argument
+        debug=False,
         input_file_path=final_barcodes_csv_fn,
-        chunk_size=100,  # Add chunk_size, default from CLI is 100 unless specified
+        chunk_size=100,
         output_file_path=final_barcode_plot_fn,
     )
 
@@ -511,6 +513,7 @@ def test_barcode_command_debug_flag(runner, temp_files, mocker):
     )
 
     mock_process_reroot.assert_called_once_with(
+        debug=True,
         sample_muts_path=matutils_S_output_fn,
         reference_fasta_path=temp_files["ref_genome"],
         sequences_fasta_path=temp_files["alignment"],
@@ -522,12 +525,12 @@ def test_barcode_command_debug_flag(runner, temp_files, mocker):
         debug=True,
         input_file_path=rerooted_lineage_paths_fn,
         output_file_path=final_barcodes_csv_fn,
-        prefix="",  # Default prefix ""
+        prefix="",
     )
     mock_create_plot.assert_called_once_with(
-        debug=True,  # Add the debug argument, should be True here
+        debug=True,
         input_file_path=final_barcodes_csv_fn,
-        chunk_size=100,  # Add chunk_size, default from CLI is 100
+        chunk_size=100,
         output_file_path=final_barcode_plot_fn,
     )
 

tests/test_ref_muts.py

@@ -195,6 +195,7 @@ def test_process_and_reroot_lineages_ref_present(
     output_rerooted_lineages = tmp_path / "rerooted_lineages.tsv"
 
     process_and_reroot_lineages(
+        debug=False,
         sample_muts_path=str(muts_file_ref_present),
         reference_fasta_path=sample_ref_fasta_file,
         sequences_fasta_path=sample_seqs_fasta_file,  # sampleA is in here
@@ -265,6 +266,7 @@ def test_process_and_reroot_lineages_ref_not_in_muts_infer_root(
     mocker.patch("barcodeforge.ref_muts.console", mocked_console)
 
     process_and_reroot_lineages(
+        debug=False,
         sample_muts_path=str(muts_file),
         reference_fasta_path=sample_ref_fasta_file,  # ref_genome AAAAAAAAAA
         sequences_fasta_path=str(seqs_file),
@@ -349,6 +351,7 @@ def test_process_and_reroot_lineages_value_error_empty_root_seqs(
         match="No valid root sequences could be generated. Check input FASTA and sample mutations.",
     ):
         process_and_reroot_lineages(
+            debug=False,
             sample_muts_path=str(muts_file),
             reference_fasta_path=sample_ref_fasta_file,
             sequences_fasta_path=str(seqs_file),
@@ -385,6 +388,7 @@ def test_process_and_reroot_lineages_warning_missing_sample_in_fasta(
     # Additional muts (ref vs inferred): none
     # Rerooted paths: original
     process_and_reroot_lineages(
+        debug=False,
         sample_muts_path=str(muts_file),
         reference_fasta_path=sample_ref_fasta_file,
         sequences_fasta_path=str(seqs_file),