Merge pull request #128 from EBI-Metagenomics/dev

Dev

Author: tgurbich

README.md

@@ -0,0 +1,19 @@
+{
+  "ftp": [
+      "genomes-all_metadata.tsv", 
+      "all_genomes", 
+      "species_catalogue", 
+      "all_genomes.msh"
+  ],
+  "additional_data": [
+      "panaroo_output", 
+      "mgyg_genomes",
+    {
+      "intermediate_files": [
+          "extra_weight_table.txt", 
+          "renamed_genomes_name_mapping.tsv"
+      ]
+    }
+  ]
+}
+

assets/output_folder_structure.json

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# coding=utf-8
+
+# This file is part of MGnify genome analysis pipeline.
+#
+# MGnify genome analysis pipeline 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.
+
+# MGnify genome analysis pipeline 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 MGnify genome analysis pipeline. If not, see <https://www.gnu.org/licenses/>.
+
+import argparse
+import os
+
+
+def main(remove_list_file, add_list_file, message, output_file):
+    already_in_remove_list = set()
+    if os.path.isfile(remove_list_file):
+        with open(remove_list_file, 'r') as file_in, open(output_file, "w") as file_out:
+            for line in file_in:
+                if line.startswith("MGYG"):
+                    file_out.write(line)
+                    accession = line.split('\t')[0].strip()
+                    already_in_remove_list.add(accession)
+
+    with open(add_list_file, 'r') as file_in, open(output_file, 'a') as file_out:
+        for line in file_in:
+            accession = line.strip()
+            if accession not in already_in_remove_list:
+                file_out.write(f"{accession}\t{message}\n")
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Script adds genomes that existed in the previous version of a '
+                                                 'catalogue but failed QC checks during the update to the remove '
+                                                 'list. Only genomes that are not already present in the remove '
+                                                 'list are added.')
+    parser.add_argument('-r', '--remove-list', required=True,
+                        help='Path to the file containing the list of genomes to remove. File should be tab-delimited '
+                             'with the MGYG accession in the first column and reason for removal in the second.')
+    parser.add_argument('-a', '--add-list', required=True,
+                        help='Path to the file containing the list of genomes to add to the remove list.')
+    parser.add_argument('-m', '--message', required=True,
+                        help='Reason for removal that will be printed to the remove file.')
+    parser.add_argument('-o', '--output', required=True,
+                        help='Name of the output file.')
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+    args = parse_args()
+    main(args.remove_list, args.add_list, args.message, args.output)
+