Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder
comparison 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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| 0:8ad77a9dc91d | 1:9ef108e34063 |
|---|---|
| 141 os.makedirs(output_tar_path) | 141 os.makedirs(output_tar_path) |
| 142 os.makedirs(output_path) | 142 os.makedirs(output_path) |
| 143 with open(output_tar_path_file, 'wb') as output_dir: | 143 with open(output_tar_path_file, 'wb') as output_dir: |
| 144 output_dir.write(request_info.content) | 144 output_dir.write(request_info.content) |
| 145 untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name)) | 145 untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name)) |
| 146 | 146 self.moove_download_files(source=untar_output, destination=output_path) |
| 147 self.moove_download_files(older_path=untar_output, new_path=output_path) | |
| 148 except requests.exceptions.HTTPError as http_error: | 147 except requests.exceptions.HTTPError as http_error: |
| 149 print(f"Requests Error: {http_error}") | 148 print(f"Requests Error: {http_error}") |
| 150 print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}") | 149 print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}") |
| 151 | 150 |
| 152 def moove_download_files(self, older_path, new_path, expression_search="*fsa"): | 151 def moove_download_files(self, source, destination, expression_search="*"): |
| 153 """ | 152 """ |
| 154 Clean downloaded data by mooving fasta files in the final folder | 153 Clean downloaded data by mooving fasta files in the final folder |
| 155 @older_path: previous path where the files are located | 154 @older_path: previous path where the files are located |
| 156 @new_path: final path where files will be mooved | 155 @new_path: final path where files will be mooved |
| 157 @expression_search: keep only file with this expression | 156 @expression_search: keep only file with this expression |
| 158 """ | 157 """ |
| 159 fasta_files = Path(older_path).rglob(expression_search) | 158 fasta_files = Path(source).rglob(expression_search) |
| 160 file_list_paths = [file for file in fasta_files if file.is_file()] | 159 file_list_paths = [file for file in fasta_files if file.is_file()] |
| 161 [self.keep_filename(pathname=path, output_path=new_path) for path in file_list_paths] | 160 [self.keep_filename(pathname=path, output_path=destination) for path in file_list_paths] |
| 162 | 161 |
| 163 def keep_filename(self, pathname, output_path): | 162 def keep_filename(self, pathname, output_path): |
| 164 """ | 163 """ |
| 165 Moove files | 164 Moove files |
| 166 @pathname: previous path | 165 @pathname: previous path |