add func to view sample coverages after wex

dereneaton · Nov 25, 2024 · d66b4ea · d66b4ea
1 parent 9bbdf98
commit d66b4ea
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/ipyrad/analysis/window_extracter.py b/ipyrad/analysis/window_extracter.py
@@ -748,6 +748,13 @@ def _write_to_nex(self):
         with open(self.outfile, 'w') as out:
             out.write("".join(lines))
 
+    def get_sample_stats(self):
+        """Return dataframe with nsites and %missing per sample."""
+        data = pd.DataFrame(index=self.allnames, columns=["nsites", "percent_missing"])
+        data["nsites"] = np.sum(self.seqarr != 78, axis=1)
+        data["percent_missing"] = data["nsites"] / self.seqarr.shape[1]
+        return data
+
 
 
 @njit()