added mt molecules and percent (#77)

* added mt molecules and percent * added mt molecules and percent * Update src/sctools/metrics/aggregator.py Co-authored-by: Jessica Way <[email protected]> * Update src/sctools/metrics/aggregator.py Co-authored-by: Jessica Way <[email protected]> Co-authored-by: Jessica Way <[email protected]>
HumanCellAtlas · May 21, 2020 · 0a8c4df · 0a8c4df
1 parent 9e198aa
commit 0a8c4df
Showing 1 changed file with 18 additions and 0 deletions.
diff --git a/src/sctools/metrics/aggregator.py b/src/sctools/metrics/aggregator.py
@@ -414,6 +414,10 @@ class CellMetrics(MetricAggregator):
         The number of genes that are observed by more than one read in this cell
     n_mitochondrial_genes: int
         The number of mitochondrial genes detected by this cell
+    n_mitochondrial_molecules: int
+        The number of molecules from mitochondrial genes detected for this cell
+    pct_mitochondrial_molecules: int
+        The percentage of molecules from mitochondrial genes detected for this cell
 
     """
 
@@ -453,6 +457,8 @@ def __init__(self):
         self.n_genes: int = None
         self.genes_detected_multiple_observations: int = None
         self.n_mitochondrial_genes: int = None
+        self.n_mitochondrial_molecules: int = None
+        self.pct_mitochondrial_molecules: float = None
 
     def finalize(self, mitochondrial_genes=set()):
         super().finalize()
@@ -471,6 +477,18 @@ def finalize(self, mitochondrial_genes=set()):
             1 for g in self._genes_histogram.keys() if g in mitochondrial_genes
         )
 
+        self.n_mitochondrial_molecules: int = sum(
+            c for g, c in self._genes_histogram.items() if g in mitochondrial_genes
+        )
+
+        if self.n_mitochondrial_molecules:
+            tot_molecules = sum(self._genes_histogram.values())
+            self.pct_mitochondrial_molecules = (
+                self.n_mitochondrial_molecules / tot_molecules * 100.0
+            )
+        else:
+            self.pct_mitochondrial_molecules = 0.00
+
     def parse_extra_fields(
         self, tags: Sequence[str], record: pysam.AlignedSegment
     ) -> None: