Updated qc_checkers/error_rate file to show if index reads

Molmed · Feb 27, 2025 · c24929c · c24929c
1 parent 8d1b752
commit c24929c
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Showing 2 changed files with 20 additions and 13 deletions.
diff --git a/checkQC/qc_checkers/error_rate.py b/checkQC/qc_checkers/error_rate.py
@@ -21,34 +21,41 @@ def error_rate(
         or error_threshold > warning_threshold
     )
 
-    def _qualify_error(error, lane, read):
+    def _qualify_error(error, lane, read, is_index_read):
         data = {
             "lane": lane,
             "read": read,
             "error": error,
         }
-        msg = "Error rate {error} > {threshold} on lane {lane} for read {read}."
+        read_or_index_text = "read (I)" if is_index_read else "read"
+        msg = "Error rate {error} > {threshold} on lane {lane} for {read_or_index_text} {read}."
 
         match error:
             case error if (np.isnan(error) or error == 0.) and not allow_missing_error_rate:
                 return QCErrorFatal(
-                    f"Error rate is {error} on lane {lane} for read {read}. "
+                    f"Error rate is {error} on lane {lane} for {read_or_index_text} {read}. "
                     "This may be because no PhiX was loaded on this lane. "
                     "Use \"allow_missing_error_rate: true\" to disable this error message.",
                     data=data,
                 )
             case error if error_threshold != "unknown" and error > error_threshold:
                 data["threshold"] = error_threshold
-                return QCErrorFatal(msg.format(**data), data=data)
+                return QCErrorFatal(
+                    msg.format(**data, read_or_index_text=read_or_index_text),
+                    data=data
+                )
             case error if warning_threshold != "unknown" and error > warning_threshold:
                 data["threshold"] = warning_threshold
-                return QCErrorWarning(msg.format(**data), data=data)
+                return QCErrorWarning(
+                    msg.format(**data, read_or_index_text=read_or_index_text),
+                    data=data
+                )
 
     return [
         qc_report
         for lane, lane_data in qc_data.sequencing_metrics.items()
         for read, read_data in lane_data["reads"].items()
-        if (qc_report := _qualify_error(read_data["mean_error_rate"], lane, read))
+        if (qc_report := _qualify_error(read_data["mean_error_rate"], lane, read, read_data["is_index"]))
     ]
 
 
diff --git a/tests/qc_checkers/test_error_rate.py b/tests/qc_checkers/test_error_rate.py
@@ -16,24 +16,24 @@ def qc_data_and_exp_val():
             {
                 1: {
                     "reads": {
-                        1: {"mean_error_rate": 0.},
-                        2: {"mean_error_rate": 110.},
-                        3: {"mean_error_rate": np.nan},
+                        1: {"mean_error_rate": 0., "is_index": True},
+                        2: {"mean_error_rate": 110., "is_index": False},
+                        3: {"mean_error_rate": np.nan, "is_index": False},
                     },
                 },
                 2: {
                     "reads": {
-                        1: {"mean_error_rate": 11.},
-                        2: {"mean_error_rate": 110.},
-                        3: {"mean_error_rate": 9.},
+                        1: {"mean_error_rate": 11., "is_index": False},
+                        2: {"mean_error_rate": 110., "is_index": False},
+                        3: {"mean_error_rate": 9., "is_index": False},
                     },
                 },
             }
         ),
         {
             1: {
                 1: QCErrorFatal(
-                    "Error rate is 0.0 on lane 1 for read 1. "
+                    "Error rate is 0.0 on lane 1 for read (I) 1. "
                     "This may be because no PhiX was loaded on this lane. "
                     "Use \"allow_missing_error_rate: true\" to disable this error message.",
                     data={"lane": 1, "read": 1, "error": 0.},