Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder
diff data_manager/plasmidfinder_fetch_database.py @ 1:9ef108e34063 draft
planemo upload commit 32f035f6404452fc8a1cf01d71be3c0b46548338
author | pimarin |
---|---|
date | Wed, 15 Feb 2023 10:35:15 +0000 |
parents | 8ad77a9dc91d |
children | bd56ac4cca16 |
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--- a/data_manager/plasmidfinder_fetch_database.py Tue Feb 14 14:25:43 2023 +0000 +++ b/data_manager/plasmidfinder_fetch_database.py Wed Feb 15 10:35:15 2023 +0000 @@ -143,22 +143,21 @@ with open(output_tar_path_file, 'wb') as output_dir: output_dir.write(request_info.content) untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name)) - - self.moove_download_files(older_path=untar_output, new_path=output_path) + self.moove_download_files(source=untar_output, destination=output_path) except requests.exceptions.HTTPError as http_error: print(f"Requests Error: {http_error}") print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}") - def moove_download_files(self, older_path, new_path, expression_search="*fsa"): + def moove_download_files(self, source, destination, expression_search="*"): """ Clean downloaded data by mooving fasta files in the final folder @older_path: previous path where the files are located @new_path: final path where files will be mooved @expression_search: keep only file with this expression """ - fasta_files = Path(older_path).rglob(expression_search) + fasta_files = Path(source).rglob(expression_search) file_list_paths = [file for file in fasta_files if file.is_file()] - [self.keep_filename(pathname=path, output_path=new_path) for path in file_list_paths] + [self.keep_filename(pathname=path, output_path=destination) for path in file_list_paths] def keep_filename(self, pathname, output_path): """