Speed up function

src/chanjo2/endpoints/coverage.py

@@ -53,8 +53,8 @@ def d4_interval_coverage(query: FileCoverageQuery):
     if None in [query.start, query.end]:  # Coverage over an entire chromosome
         return IntervalCoverage(
             mean_coverage=get_d4tools_chromosome_mean_coverage(
-                d4_file_path=query.coverage_file_path, chromosome=query.chromosome
-            ),
+                d4_file_path=query.coverage_file_path, chromosomes=[query.chromosome]
+            )[0][1],
             completeness={},
             interval_id=interval,
         )

src/chanjo2/meta/handle_d4.py

@@ -46,18 +46,23 @@ def get_intervals_coords_list(
     return interval_coords
 
 
-def get_d4tools_chromosome_mean_coverage(d4_file_path: str, chromosome=str) -> float:
-    """Return mean coverage over one entire chromosome."""
+def get_d4tools_chromosome_mean_coverage(
+    d4_file_path: str, chromosomes=List[str]
+) -> List[Tuple[str, float]]:
+    """Return mean coverage over entire chromosomes."""
 
     chromosomes_stats_mean_cmd: List[str] = subprocess.check_output(
         ["d4tools", "stat", "-s" "mean", d4_file_path],
         text=True,
     ).splitlines()
-
+    chromosomes_coverage: List[Tuple[str, float]] = []
     for line in chromosomes_stats_mean_cmd:
         stats_data: List[str] = line.split("\t")
-        if chromosome == stats_data[CHROM_INDEX]:
-            return float(stats_data[STATS_MEAN_COVERAGE_INDEX])
+        if stats_data[CHROM_INDEX] in chromosomes:
+            chromosomes_coverage.append(
+                (stats_data[CHROM_INDEX], float(stats_data[STATS_MEAN_COVERAGE_INDEX]))
+            )
+    return chromosomes_coverage
 
 
 def get_d4tools_intervals_mean_coverage(
@@ -345,17 +350,14 @@ def predict_sex(x_cov: float, y_cov: float) -> str:
 def get_samples_sex_metrics(d4_file_path: str) -> Dict:
     """Compute coverage over sex chromosomes and predicted sex."""
 
-    sex_chroms_coverage: List[float] = [
-        get_d4tools_chromosome_mean_coverage(
-            d4_file_path=d4_file_path, chromosome=chrom
-        )
-        for chrom in ["X", "Y"]
-    ]
+    sex_chroms_coverage: List[Tuple[str, float]] = get_d4tools_chromosome_mean_coverage(
+        d4_file_path=d4_file_path, chromosomes=["X", "Y"]
+    )
 
     return {
-        "x_coverage": round(sex_chroms_coverage[0], 1),
-        "y_coverage": round(sex_chroms_coverage[1], 1),
+        "x_coverage": round(sex_chroms_coverage[0][1], 1),
+        "y_coverage": round(sex_chroms_coverage[1][1], 1),
         "predicted_sex": predict_sex(
-            x_cov=sex_chroms_coverage[0], y_cov=sex_chroms_coverage[1]
+            x_cov=sex_chroms_coverage[0][1], y_cov=sex_chroms_coverage[1][1]
         ),
     }