Added a qc reporting file

primalscheme3/__init__.py

@@ -1 +1 @@
-__version__ = "3.0.0"
+__version__ = "3.0.1"

primalscheme3/core/config.py

@@ -124,6 +124,14 @@ def __str__(self) -> str:
 
     def assign_kwargs(self, **kwargs: Any) -> None:
         for key, value in kwargs.items():
+            # Check if key is valid
+            if value is None:
+                continue
+
+            if key == "input_bedfile":
+                setattr(self, key, pathlib.Path(value))
+                continue
+
             if hasattr(self, key):
                 # Convert to expected type
                 if isinstance(getattr(self, key), MappingType):

primalscheme3/core/multiplex.py

@@ -211,6 +211,28 @@ def get_coverage_percent(self, msa_index: int) -> float:
             self._coverage[msa_index].sum() / len(self._coverage[msa_index]) * 100, 2
         )
 
+    def get_coverage_gaps(self, msa_index: int) -> list[tuple[int, int]]:
+        """
+        Returns the coverage gaps for the specified MSA index
+        :param msa_index: int
+        :return: list[tuple[int, int]]
+        """
+        gaps = []
+        in_gap = False
+        gap_start = 0
+        for i, covered in enumerate(self._coverage[msa_index]):
+            if not covered:
+                if not in_gap:
+                    gap_start = i
+                    in_gap = True
+            else:
+                if in_gap:
+                    gaps.append((gap_start, i))
+                    in_gap = False
+        if in_gap:
+            gaps.append((gap_start, i))
+        return gaps
+
     def update_coverage(self, primerpair: PrimerPair, add: bool = True) -> None:
         """
         Updates the coverage for the specified MSA index

primalscheme3/scheme/scheme_main.py

@@ -454,7 +454,7 @@ def schemecreate(
     for msa_index, msa_obj in msa_dict.items():
         # Set up the pm for the MSA
         scheme_pt = pm.create_sub_progress(
-            iter=None, chrom=msa_obj._chrom_name, process="Creating Scheme", leave=False
+            iter=None, chrom=msa_obj.name, process="Creating Scheme", leave=False
         )
         scheme_pt.manual_update(n=0, total=msa_obj.array.shape[1])
 
@@ -602,6 +602,19 @@ def schemecreate(
 
     upload_pt.manual_update(n=4, update=True)
 
+    # Create qc coverage data
+    qc_data = {}
+    for msa_index, msa_obj in msa_dict.items():
+        msa_data = {"coverage": scheme.get_coverage_percent(msa_index)}
+        msa_data["n_amplicons"] = len(
+            [x for x in scheme._last_pp_added if x.msa_index == msa_index]
+        )
+        msa_data["n_gaps"] = len(scheme.get_coverage_gaps(msa_index))
+        qc_data[msa_obj.name] = msa_data
+
+    with open(OUTPUT_DIR / "work" / "qc.json", "w") as outfile:
+        outfile.write(json.dumps(qc_data, sort_keys=True))
+
     ## DO THIS LAST AS THIS CAN TAKE A LONG TIME
     # Writing plot data
     plot_data = generate_all_plotdata(

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "primalscheme3"
-version = "3.0.0"
+version = "3.0.1"
 description = ""
 authors = ["ChrisKent <[email protected]>"]
 readme = "README.md"