Add Coverage Statistics Calculation Script for Mosdepth

docker/lr-mosdepth/Dockerfile

@@ -18,3 +18,6 @@ RUN curl https://sdk.cloud.google.com | bash
 
 # activate conda environment
 RUN echo "source activate lr-mosdepth" > ~/.bashrc
+
+# copy the script
+COPY coverage_stats.py /

docker/lr-mosdepth/coverage_stats.py

@@ -0,0 +1,166 @@
+import argparse
+import gzip
+import json
+import logging
+
+import numpy as np
+import pandas as pd
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(description="Process coverage values.")
+    parser.add_argument("mosdepth_regions", type=str,
+                        help="Mosdepth output file containing coverage values.")
+    parser.add_argument("--cov_col", type=int, default=4,
+                        help="Column holding the coverage values.")
+    parser.add_argument("--output_prefix", type=str,
+                        help="Prefix to use for output files.")
+    parser.add_argument("--round", type=int, default=2, help="Rounding precision.")
+    parser.add_argument("--debug", action="store_true", help="Debug mode.")
+    return parser.parse_args()
+
+
+def calculate_summary_statistics(
+        df: pd.DataFrame, cov_col: int, round_precision: int
+) -> dict:
+    """
+    Calculate summary statistics for the coverage values.
+    @param df: Dataframe containing coverage values
+    @param cov_col: Column containing coverage values
+    @param round_precision: Rounding precision
+    @return:
+    """
+
+    cov_data: pd.Series = df.iloc[:, cov_col - 1]
+    mean_val: float = cov_data.mean()
+    mad_val: float = np.mean(np.abs(cov_data - mean_val))
+
+    statistics = {
+        "cov_mean": round(mean_val, round_precision),
+        "cov_q1": round(cov_data.quantile(0.25), round_precision),
+        "cov_median": round(cov_data.median(), round_precision),
+        "cov_q3": round(cov_data.quantile(0.75), round_precision),
+        "cov_iqr": round(cov_data.quantile(0.75) - cov_data.quantile(0.25), round_precision),
+        "cov_stdev": round(cov_data.std(), round_precision),
+        "cov_mad": round(mad_val, round_precision),
+        "cov_percent_above_4x": percentage_greater_than_4x(df, cov_col, round_precision),
+        "cov_evenness_score": calculate_evenness_score(df, cov_col, round_precision)
+    }
+
+    # Replace Nan values with null
+    for key, value in statistics.items():
+        if pd.isna(value):
+            statistics[key] = "null"
+
+    return statistics
+
+
+def percentage_greater_than_4x(
+        df: pd.DataFrame, cov_col: int, round_precision: int
+) -> float:
+    """
+    Calculate the percentage of coverage values greater than 4x.
+    @param df: Dataframe containing coverage values
+    @param cov_col: Column containing coverage values
+    @param round_precision: Rounding precision
+    @return:
+    """
+    logging.debug("Calculating percentage of coverage values greater than 4x")
+    total_bases = len(df)
+    bases_above_4x = df[df.iloc[:, cov_col - 1] > 4].shape[0]
+    percent_above_4x = round(bases_above_4x / total_bases, round_precision)
+
+    logging.info("Percentage of coverage values greater than 4x: %s", percent_above_4x)
+
+    return percent_above_4x
+
+
+def calculate_evenness_score(
+        df: pd.DataFrame, cov_col: int, round_precision: int) -> float:
+    """
+    Calculate the evenness score.
+    Konrad Oexle, Journal of Human Genetics 2016, Evaulation of the evenness score in NGS.
+    https://www.nature.com/articles/jhg201621
+
+    @param df: Dataframe containing coverage values
+    @param cov_col: Column containing coverage values
+    @param round_precision: Rounding precision
+    @return:
+    """
+    logging.debug("Calculating evenness score")
+    mean_coverage = df.iloc[:, cov_col - 1].mean()
+    # Get the coverage values that are less than or equal to the mean coverage
+    d2 = df[df.iloc[:, cov_col - 1] <= mean_coverage].iloc[:, cov_col - 1].tolist()
+    # count of coverage values that are less than or equal to the mean coverage
+    d2_count = len(d2)
+    # sum of coverage values that are less than or equal to the mean coverage
+    d2_sum = sum(d2)
+    # total number of coverages
+    coverage_count = len(df)
+
+    logging.debug("Mean coverage: %s", mean_coverage)
+    logging.debug("D2 count: %s", d2_count)
+    logging.debug("D2 sum: %s", d2_sum)
+    logging.debug("Coverage count: %s", coverage_count)
+
+    if mean_coverage != 0:
+        evenness_score = round(1 - (d2_count - (d2_sum / mean_coverage)) / coverage_count, round_precision)
+    else:
+        logging.warning("Mean coverage is zero. Evenness score will be set to null.")
+        evenness_score = "null"
+
+    logging.info("Evenness score: %s", evenness_score)
+
+    return evenness_score
+
+
+def open_file(file_path: str) -> pd.DataFrame:
+    """
+    Open a file and return a dataframe
+    @param file_path: Path to the file
+    @return:
+    """
+
+    if file_path.endswith(".gz"):
+        with gzip.open(file_path, "rt") as f:
+            df = pd.read_csv(f, sep="\t", header=None)
+    else:
+        with open(file_path, "rt") as f:
+            df = pd.read_csv(f, sep="\t", header=None)
+
+    return df
+
+
+def main():
+    args = parse_arguments()
+    if args.debug:
+        logging.basicConfig(level=logging.DEBUG)
+    else:
+        logging.basicConfig(level=logging.INFO)
+
+    logging.info("Arguments: %s", args)
+    logging.info("Calculating coverage statistics")
+
+    prefix = args.output_prefix if args.output_prefix else args.mosdepth_regions.split(".")[0]
+
+    df: pd.DataFrame = open_file(args.mosdepth_regions)
+    logging.info("Opened file: %s", args.mosdepth_regions)
+
+    logging.debug("Dataframe shape: %s", df.shape)
+    logging.debug("Dataframe columns: %s", df.columns)
+    logging.debug(f"Dataframe Head\n{df.head()}")
+
+    statistics = calculate_summary_statistics(df, args.cov_col, args.round)
+
+    logging.info("Summary statistics: %s", statistics)
+
+    summary_file = f"{prefix}.cov_stat_summary.json"
+
+    logging.info("Writing summary statistics to file: %s", summary_file)
+    with open(summary_file, "w") as f:
+        json.dump(statistics, f)
+        f.write("\n")
+
+
+if __name__ == "__main__":
+    main()

docker/lr-mosdepth/environment.yml

@@ -44,6 +44,8 @@ dependencies:
   - pyvcf=0.6.8=py36_0
   - readline=8.1=h27cfd23_0
   - samtools=1.11=h6270b1f_0
+  - numpy=1.19.5
+  - pandas=1.1.5
   - setuptools=52.0.0=py36h06a4308_0
   - six=1.15.0=py36h06a4308_0
   - sqlite=3.35.4=hdfb4753_0