Mercurial > repos > bebatut > data_manager_sortmerna_database_downloader
changeset 11:01d511f950d9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit a17ff4bb67251145f59ed1f4b437b4950308db08-dirty
| author | bebatut |
|---|---|
| date | Mon, 12 Jun 2017 10:50:07 -0400 |
| parents | d2a91cfb9eef |
| children | 1cb13ad2d59b |
| files | data_manager/data_manager_sortmerna_download.py |
| diffstat | 1 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/data_manager_sortmerna_download.py Mon Jun 12 10:25:42 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.py Mon Jun 12 10:50:07 2017 -0400 @@ -126,12 +126,14 @@ if not filename.endswith("fasta"): continue input_filepath = os.path.join(file_dir, filename) - output_dir = os.path.join(target_dir, filename) - os.mkdir(output_dir) + # Extract the db name db_name = os.path.splitext(filename)[0] - fasta_filepath = os.path.join(output_dir, "%s.fasta" % db_name) - indexed_filepath = os.path.join(output_dir, db_name) - # Move file + # Create the directory where to put the fasta files and indexed files + filedir = os.path.join(target_dir, filename) + os.mkdir(filedir) + fasta_filepath = os.path.join(filedir, "%s.fasta" % db_name) + indexed_filepath = os.path.join(filedir, db_name) + # Move the fasta file os.rename(input_filepath, fasta_filepath) # Index the file with indexdb_rna command = "indexdb_rna --ref %s,%s" % (