Added script extracting first positions from bed.

scripts/extract_annot_start.py

+#!/usr/bin/env python3
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""Extracts the first N positions from the annotations provided in a bed file.
+
+The result is written in bed format on the standard output.
+No bounds checks are performed. Some resulting bed entries might exceed
+chromosome boundaries.
+"""
+
+from argparse import (
+    ArgumentParser,
+    ArgumentDefaultsHelpFormatter)
+import sys
+
+
+def main():
+    """Run the command-line script."""
+    parser = ArgumentParser(
+        description=__doc__,
+        formatter_class=ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "-b", "--bedfile",
+        required=True,
+        help="Input bed file.")
+    parser.add_argument(
+        "-s", "--start_size",
+        type=int,
+        default=200,
+        help="Number of positions to extract.")
+    parser.add_argument(
+        "-k", "--keep_short",
+        help="Set this option to keep annotations that are too short.",
+        action="store_true")
+    args = parser.parse_args()
+
+    start_size = args.start_size
+    keep_short = args.keep_short
+    nb_too_short = 0
+    with open(args.bedfile) as bedfile:
+        for line in bedfile:
+            (chrom, start, end, name, score, strand) = line.strip().split("\t")
+            if int(end) - int(start) < start_size:
+                nb_too_short += 1
+                if keep_short:
+                    sys.stderr.write(
+                        "Extracted fragment will be longer "
+                        f"than annotation size for {name}\n")
+                else:
+                    continue
+            if strand == "-":
+                print(
+                    chrom, int(end) - start_size, int(end),
+                    name, score, strand, sep="\t")
+            else:
+                print(
+                    chrom, int(start), int(start) + start_size,
+                    name, score, strand, sep="\t")
+    if nb_too_short:
+        sys.stderr.write(
+            f"{nb_too_short} annotations were shorter "
+            "than the extracted fragment.\n")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())