Mercurial > repos > jpayne > bioproject_to_srr_2
comparison bio2srr.py @ 15:0a3943480712
planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538
| author | jpayne |
|---|---|
| date | Tue, 21 May 2024 01:05:30 -0400 |
| parents | fc77995bc4da |
| children |
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| 14:18e1cb6018fd | 15:0a3943480712 |
|---|---|
| 255 logger.warning(f"Some SRA runs may have been reached through multiple projects or samples. accessions.txt will be deduplicated but the metadata table is not") | 255 logger.warning(f"Some SRA runs may have been reached through multiple projects or samples. accessions.txt will be deduplicated but the metadata table is not") |
| 256 | 256 |
| 257 log(f"Writing {len(accessions)} unique accessions to accessions.txt") | 257 log(f"Writing {len(accessions)} unique accessions to accessions.txt") |
| 258 | 258 |
| 259 with open("accessions.txt", "w") as f: | 259 with open("accessions.txt", "w") as f: |
| 260 f.writelines(accessions) | 260 for accession in accessions: |
| 261 f.write(accession + "\n") | |
| 261 | 262 |
| 262 | 263 |
| 263 if __name__ == "__main__": | 264 if __name__ == "__main__": |
| 264 b = sys.argv[1].strip() | 265 b = sys.argv[1].strip() |
| 265 log(f"Starting with {b}") | 266 log(f"Starting with {b}") |