Added an empty mobilome clean up script

helpers/remove_empty_mobilome_files.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# Copyright 2024 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import argparse
+import glob
+import os
+
+
+def main(results_folder):
+ pattern = os.path.join(results_folder, "species_catalogue", '**', '*_mobilome.gff')
+ all_matching_files = glob.glob(pattern, recursive=True)
+ filtered_files = [file for file in all_matching_files if os.path.basename(file).count('_') == 1]
+ for mobilome_file in filtered_files:
+ file_has_contents = evaluate_file(mobilome_file)
+ if not file_has_contents:
+ print("Cleaning {}".format(mobilome_file))
+ with open(mobilome_file, "w") as f_out:
+ f_out.write("##gff-version 3\n")
+
+
+def evaluate_file(mobilome_file):
+ with open(mobilome_file, 'r') as f:
+ for line in f:
+ if line.startswith("##FASTA"):
+ return False
+ elif not line.startswith("##"):
+ return True
+
+
+def parse_args():
+ parser = argparse.ArgumentParser(
+ description="The script goes through the catalogue results folder and replaces the mobilome GFF with "
+ "an empty, header-only GFF file if there are no mobilome lines in it. This is to account "
+ "for the fact that the mobilome pipeline outputs a file with just the headers and the original "
+ "fasta sequences if there are no mobilome results."
+ )
+ parser.add_argument(
+ "-i", "--input-directory",
+ required=True,
+ help="Path to the catalogue results folder",
+ )
+ return parser.parse_args()
+
+
+if __name__ == "__main__":
+ args = parse_args()
+ main(args.input_directory)
+