Several small bug fixes

src/pmotools/pmo_builder/metatable_to_pmo.py

@@ -157,7 +157,7 @@ def library_sample_info_table_to_pmo(
         library_prep_plate_position_col,
         meta_json,
         copy_contents,
-        "specimen_name",
+        "library_sample_name",
         "library_prep_plate_info",
     )
     meta_json = add_parasite_density_info(
@@ -166,7 +166,7 @@ def library_sample_info_table_to_pmo(
         meta_json,
         copy_contents,
         "library_sample_name",
-        entry_name="parasite_density_info",
+        entry_name="qpcr_parasite_density_info",
     )
     # listify columns that contain values that could be list, are delimited by the argument list_values_library_values_delimiter
     primitives = (int, float, str, bool, complex)
@@ -494,7 +494,7 @@ def add_plate_info(
     plate_position_col,
     meta_json,
     df,
-    specimen_name_col,
+    match_col,
     entry_name="plate_info",
 ):
     if all(
@@ -531,7 +531,7 @@ def add_plate_info(
                 ) from e
 
     for row in meta_json:
-        content_row = df[df[specimen_name_col] == row[specimen_name_col]]
+        content_row = df[df[match_col] == row[match_col]]
         plate_name_val = content_row[plate_name_col].iloc[0] if plate_name_col else None
         plate_row_val = (
             content_row[plate_row_col].iloc[0].upper() if plate_row_col else None
@@ -560,7 +560,7 @@ def add_parasite_density_info(
     parasite_density_method_col,
     meta_json,
     df,
-    specimen_name_col,
+    match_col,
     entry_name,
 ):
     density_method_pairs = []
@@ -608,7 +608,7 @@ def add_parasite_density_info(
 
     # Add parasite density info to meta_json
     for row in meta_json:
-        content_row = df[df[specimen_name_col] == row[specimen_name_col]]
+        content_row = df[df[match_col] == row[match_col]]
         density_infos = []
         for density_col, method_col in density_method_pairs:
             density_val = content_row[density_col].iloc[0] if density_col else None

src/pmotools/pmo_builder/panel_information_to_pmo.py

@@ -332,8 +332,8 @@ def build_target_info_dict(
                 fwd_primer_dict["location"] = {
                     "genome_id": genome_id,
                     "chrom": row[chrom_col],
-                    "end": int(row[forward_primers_start_col]),
-                    "start": int(row[forward_primers_end_col]),
+                    "start": int(row[forward_primers_start_col]),
+                    "end": int(row[forward_primers_end_col]),
                 }
                 if strand_col and pd.notna(row[strand_col]):
                     fwd_primer_dict["location"]["strand"] = row[strand_col]

src/pmotools/pmo_engine/pmo_exporter.py

@@ -451,6 +451,7 @@ def write_bed_locs(bed_locs: list[BedLoc], fnp, add_header: bool = False):
                         ]
                     )
                 )
+                f.write("\n")
             for bed_loc in bed_locs:
                 f.write(
                     "\t".join(
@@ -540,11 +541,10 @@ def extract_panels_insert_bed_loc(
         :param sort_output: whether to sort output by genomic location
         :return: a list of target inserts, with named tuples with fields: chrom, start, end, name, score, strand, ref_seq, extra_info
         """
-        bed_loc_out = {}
+        bed_loc_out = []
         if select_panel_ids is None:
             select_panel_ids = list(range(len(pmodata["panel_info"])))
         for panel_id in select_panel_ids:
-            bed_loc_out_per_panel = []
             for reaction_id in range(len(pmodata["panel_info"][panel_id]["reactions"])):
                 for target_id in pmodata["panel_info"][panel_id]["reactions"][
                     reaction_id
@@ -589,7 +589,7 @@ def extract_panels_insert_bed_loc(
                         if "ref_seq" not in tar["insert_location"]
                         else tar["insert_location"]["ref_seq"]
                     )
-                    bed_loc_out_per_panel.append(
+                    bed_loc_out.append(
                         BedLoc(
                             tar["insert_location"]["chrom"],
                             tar["insert_location"]["start"],
@@ -602,12 +602,8 @@ def extract_panels_insert_bed_loc(
                             extra_info,
                         )
                     )
-                if sort_output:
-                    return sorted(
-                        bed_loc_out_per_panel,
-                        key=lambda bed: (bed.chrom, bed.start, bed.end),
-                    )
-            bed_loc_out[panel_id] = bed_loc_out_per_panel
+        if sort_output:
+            return sorted(bed_loc_out, key=lambda bed: (bed.chrom, bed.start, bed.end))
         return bed_loc_out
 
     @staticmethod

tests/test_pmo_builder/test_metatable_to_pmo.py

@@ -1603,13 +1603,18 @@ def test_library_sample_info_table_to_pmo_with_parasite_density(self):
             parasite_density_method_col="parasite_density_method",
         )
 
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 10)
         self.assertEqual(
-            result[0]["parasite_density_info"][0]["parasite_density_method"], "qPCR"
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 10
         )
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 100)
         self.assertEqual(
-            result[1]["parasite_density_info"][0]["parasite_density_method"],
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density_method"],
+            "qPCR",
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 100
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density_method"],
             "microscopy",
         )
 
@@ -1638,10 +1643,18 @@ def test_library_sample_info_table_to_pmo_with_parasite_density_multiple(self):
             parasite_density_method_col=["method1", "method2"],
         )
 
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 15)
-        self.assertEqual(result[0]["parasite_density_info"][1]["parasite_density"], 10)
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 107)
-        self.assertEqual(result[1]["parasite_density_info"][1]["parasite_density"], 100)
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 15
+        )
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][1]["parasite_density"], 10
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 107
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][1]["parasite_density"], 100
+        )
 
     def test_library_sample_info_table_to_pmo_with_all_new_fields(self):
         """Test all new optional fields together"""
@@ -1685,15 +1698,19 @@ def test_library_sample_info_table_to_pmo_with_all_new_fields(self):
         self.assertEqual(result[0]["experiment_accession"], "EXP001")
         self.assertEqual(result[0]["fastqs_loc"], "/path/to/fastqs1")
         self.assertEqual(result[0]["run_accession"], "RUN001")
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 10)
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 10
+        )
         self.assertIn("library_prep_plate_info", result[0])
         self.assertEqual(result[0]["library_prep_plate_info"]["plate_col"], 1)
 
         self.assertEqual(result[1]["alternate_identifiers"], ["ID2"])
         self.assertEqual(result[1]["experiment_accession"], "EXP002")
         self.assertEqual(result[1]["fastqs_loc"], "/path/to/fastqs2")
         self.assertEqual(result[1]["run_accession"], "RUN002")
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 100)
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 100
+        )
         self.assertIn("library_prep_plate_info", result[1])
         self.assertEqual(result[1]["library_prep_plate_info"]["plate_col"], 2)
 

tests/test_pmo_builder/test_panel_information_to_pmo.py

@@ -416,8 +416,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -443,8 +443,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -470,8 +470,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -526,8 +526,8 @@ def test_build_target_info_dict_missing_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {"seq": "GTT"},

tests/test_pmo_engine/test_pmo_exporter.py

@@ -105,6 +105,54 @@ def test_extract_panels_insert_bed_loc(self):
         PMOExporter.write_bed_locs(all_target_inserts, output_fnp)
         self.assertEqual("52b1f79a3a89f8265573fa54b5a7ce57", md5sum_of_fnp(output_fnp))
 
+    def test_extract_panels_insert_bed_loc_covers_all_reactions(self):
+        # regression: previously the function returned early inside the reaction
+        # loop, so only the first reaction of the first panel was returned.
+        import copy
+
+        pmo = copy.deepcopy(self.combined_pmo_data)
+        panel = pmo["panel_info"][0]
+        targets = panel["reactions"][0]["panel_targets"]
+        half = len(targets) // 2
+        panel["reactions"] = [
+            {"reaction_name": "pool1", "panel_targets": targets[:half]},
+            {"reaction_name": "pool2", "panel_targets": targets[half:]},
+        ]
+        bed_locs = PMOExporter.extract_panels_insert_bed_loc(pmo, sort_output=False)
+        # every target across BOTH reactions is present
+        self.assertEqual(len(bed_locs), len(targets))
+        self.assertEqual(
+            {b.name for b in bed_locs},
+            {pmo["target_info"][t]["target_name"] for t in targets},
+        )
+
+    def test_write_bed_locs_header_on_own_line(self):
+        # regression: header was written without a trailing newline, gluing the
+        # first data row onto it.
+        bed_locs = PMOExporter.extract_targets_insert_bed_loc(
+            self.combined_pmo_data, sort_output=True
+        )
+        out_fnp = os.path.join(self.test_dir.name, "with_header.bed")
+        PMOExporter.write_bed_locs(bed_locs, out_fnp, add_header=True)
+        with open(out_fnp) as f:
+            lines = f.read().splitlines()
+        self.assertEqual(
+            lines[0],
+            "\t".join(
+                [
+                    "#chrom",
+                    "start",
+                    "end",
+                    "name",
+                    "score",
+                    "strand",
+                    "ref_seq",
+                    "extra_info",
+                ]
+            ),
+        )
+        self.assertEqual(len(lines), len(bed_locs) + 1)
+
     def test_extract_alleles_per_sample_table(self):
         allele_data = PMOExporter.extract_alleles_per_sample_table(
             self.combined_pmo_data,