--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dustmasker_wrapper.py	Fri Aug 04 12:35:32 2023 +0000
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+"""
+This script is used to run dustmasker on a fasta file. It will create
+a bed file from default dustmasker output.
+"""
+import argparse
+import subprocess
+import tempfile
+
+# parse arguments from command line, and pass it to duskmasker
+
+parser = argparse.ArgumentParser(
+    description="""This script is used to run dustmasker on a fasta file. It will create
+    a bed file from default dustmasker output.""",
+    formatter_class=argparse.RawTextHelpFormatter, )
+parser.add_argument(
+    '-f', '--fasta', default=None, required=True, help="fasta file", type=str,
+    action='store'
+    )
+parser.add_argument(
+    '-o', '--output', default=None, required=True, help="output file name", type=str,
+    action='store'
+    )
+parser.add_argument(
+    '-w', '--window', default=60, required=False, help="dustmasker window size", type=int,
+    action='store'
+    )
+parser.add_argument(
+    '-l', '--level', default=20, required=False, help="dustmasker level", action='store'
+    )
+args = parser.parse_args()
+
+
+def main(args):
+    """
+    run dustmasker and convert output do bed file
+    """
+    # temp file for dust maske output
+    tmpfile = tempfile.NamedTemporaryFile().name
+    # run dustmasker
+    subprocess.call(
+        ["dustmasker", "-in", args.fasta, "-out", tmpfile, "-window", str(args.window),
+         "-level", str(args.level)]
+        )
+    # create bed file from dustmasker output
+    # syntax of dustmasker output is:
+    # >contig_name
+    # start_position - end_position
+    # start_position - end_position
+    # ...
+    # if not masked, only contig name is printed
+    with open(args.output, "w") as f:
+        with open(tmpfile, "r") as f2:
+            for line in f2:
+                if line[0] == ">":
+                    contig_name = line.strip()[1:]
+                    continue
+                else:
+                    line = line.strip()
+                    line = line.split()
+                    f.write(contig_name + "\t" + line[0] + "\t" + line[2] + "\n")
+
+
+if __name__ == '__main__':
+    main(args)