Add support for only calculating coverage for cut sites instead of th…

…e whole fragment.

Add support for only calculating coverage for cut sites instead of the whole fragment.

src/scatac_fragment_tools/cli/commands.py

@@ -32,6 +32,7 @@ def command_fragment_to_bigwigs(args):
         fragments_df,
         chrom_sizes,
         args.bigwig_filename,
-        args.normalize == "yes",
+        args.normalize,
         args.scaling_factor,
+        args.cut_sites,
     )

src/scatac_fragment_tools/cli/main.py

@@ -55,12 +55,11 @@ def add_fragments_to_bigwig_subparser(
         "-n",
         "--normalize",
         dest="normalize",
-        action="store",
-        type=str,
+        action="store_true",
         required=False,
-        choices={"yes", "no"},
-        default="yes",
-        help='Normalize genome coverage data. Default: "yes".',
+        default=False,
+        help="Normalize genome coverage data by dividing by sequencing depth "
+        "(number of fragments) multiplied by 1 million.",
     )
     optional_arguments.add_argument(
         "-s",
@@ -70,7 +69,18 @@ def add_fragments_to_bigwig_subparser(
         type=float,
         required=False,
         default=1.0,
-        help='Scaling factor for genome coverage data. Default: "1.0".',
+        help="Scaling factor for genome coverage data. "
+        'If normalization is enabled, scaling is applied afterwards. Default: "1.0".',
+    )
+    optional_arguments.add_argument(
+        "-x",
+        "--cut-sites",
+        dest="cut_sites",
+        action="store_true",
+        required=False,
+        default=False,
+        help="Use 1 bp Tn5 cut sites (start and end of each fragment) instead of whole "
+        "fragment length for coverage calculation.",
     )
     optional_arguments.add_argument(
         "--chrom-prefix",

src/scatac_fragment_tools/library/bigwig/fragments_to_bigwig.py

@@ -7,13 +7,14 @@
 import numpy as np
 import polars as pl
 import pyarrow as pa
+import pyarrow.csv
 import pyBigWig
 
 
 def get_chromosome_sizes(chrom_sizes_filename: str):
     chrom_sizes = {}
 
-    with open(chrom_sizes_filename, "r") as fh:
+    with open(chrom_sizes_filename, "r") as fh:  # noqa: UP015
         for line in fh:
             line = line.rstrip("\n")
 
@@ -332,6 +333,12 @@ def fragments_to_bw(
             starts, ends = (
                 per_chrom_fragments_dfs[chrom].select(["Start", "End"]).to_numpy().T
             )
+            if cut_sites:
+                # Create cut site positions (for both start and end of a fragment).
+                starts, ends = (
+                    np.hstack((starts, ends - 1)),
+                    np.hstack((starts + 1, ends)),
+                )
             chrom_arrays[chrom] = calculate_depth(chrom_sizes[chrom], starts, ends)
             no_fragments += per_chrom_fragments_dfs[chrom].height