From 1d76a603742798b9f24ff775a4da6ca90067318f Mon Sep 17 00:00:00 2001
From: Tatiana Gurbich <tgurbich@gmail.com>
Date: Thu, 8 Aug 2024 10:34:30 +0100
Subject: [PATCH] Added an empty mobilome clean up script

---
 helpers/remove_empty_mobilome_files.py | 62 ++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 helpers/remove_empty_mobilome_files.py

diff --git a/helpers/remove_empty_mobilome_files.py b/helpers/remove_empty_mobilome_files.py
new file mode 100644
index 00000000..1c6cb7ae
--- /dev/null
+++ b/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)
+