From 1f5851abef037f9630172165bac0acbc8b79d208 Mon Sep 17 00:00:00 2001
From: Fabian groll <fabian.groll@mpi-muenster.mpg.de>
Date: Fri, 7 Aug 2020 16:43:48 +0200
Subject: [PATCH] Added command to determine resolution of Hi-C experiment

---
 fanc/commands/fanc_commands.py | 104 +++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)

diff --git a/fanc/commands/fanc_commands.py b/fanc/commands/fanc_commands.py
index 5d774bb2..936a952a 100644
--- a/fanc/commands/fanc_commands.py
+++ b/fanc/commands/fanc_commands.py
@@ -2189,6 +2189,110 @@ def dump(argv, **kwargs):
     logger.info("All done.")
 
 
+def resolution_parser():
+    parser = argparse.ArgumentParser(
+        prog='fanc resolution',
+        description='Determine the resolution of a Hi-C experiment'
+    )
+
+    parser.add_argument(
+        'input',
+        help='Directory containing binned Hi-C matrices.'
+    )
+
+    parser.add_argument(
+        'output',
+        nargs='?',
+        help='Output file for results. If not provided, will write to stdout'
+    )
+
+    parser.add_argument(
+        '-i', '--interactions-threshold',
+        type=int,
+        default=1000,
+        help='Threshold of interactions per bin. Default: %(default)d'
+    )
+
+    parser.add_argument(
+        '-t', '--threads',
+        type=int,
+        default=1,
+        help='Number of threads used for parallel processing of files. Default: %(default)d'
+    )
+
+    parser.add_argument(
+        '-p', '--plot',
+        help='Path for saving resolution plot'
+    )
+
+    return parser
+
+
+def _resolution_bins_passing_threshold(hic_file, threshold):
+    """Percentage of bins passing threshold of marginals."""
+    from fanc.tools.load import load
+
+    hic = load(hic_file, mode='r')
+    marginals = hic.marginals(masked=False, norm=False)
+    return hic.bin_size, sum(marginals > threshold) / len(marginals)
+
+
+def resolution(argv, **kwargs):
+    parser = resolution_parser()
+    args = parser.parse_args(argv[2:])
+
+    input_dir = args.input
+    output_file = os.path.expanduser(args.output) if args.output is not None else None
+    plot_file = os.path.expanduser(args.plot) if args.plot is not None else None
+    threshold = args.interactions_threshold
+    threads = args.threads
+
+    from fanc.tools.load import load
+    from fanc.tools.general import human_format
+    import glob
+    from multiprocessing import Pool
+    import sys
+
+    input_files = sorted(
+        glob.iglob(f"{input_dir}/*.hic"),
+        key=lambda file: load(file, mode='r').bin_size
+    )
+
+    with Pool(threads) as p:
+        results = p.starmap(
+            _resolution_bins_passing_threshold,
+            ((file, threshold) for file in input_files)
+        )
+
+    with open(output_file, 'w') if output_file is not None else sys.stdout as f:
+        for result, file in sorted(zip(results, input_files), reverse=True):
+            f.write(f"{os.path.basename(file)}\t{result[0]}\t{result[1]}\n")
+
+    if plot_file is not None:
+        import matplotlib
+        matplotlib.use('agg')
+        import matplotlib.pyplot as plt
+        import matplotlib.ticker as ticker
+
+        bin_size, bins_passing = list(zip(*results))
+        bins_passing = [x * 100 for x in bins_passing]
+
+        fig, ax = plt.subplots()
+        ax.plot(bin_size, bins_passing)
+        ax.axhline(80, linestyle='--', color='black')
+        ax.set_xscale('log')
+        ax.set_xticks(bin_size)
+        ax.invert_xaxis()
+        ax.xaxis.set_major_formatter(ticker.ScalarFormatter())
+        ax.xaxis.set_major_formatter(
+            ticker.FuncFormatter(lambda x, _: f"{human_format(x)}b")
+        )
+        ax.set_xlabel('Bin size')
+        ax.set_ylabel(f"Bins with > {threshold} contacts %")
+        fig.savefig(plot_file)
+        plt.close(fig)
+
+
 def pca_parser():
     parser = argparse.ArgumentParser(
         prog="fanc pca",