Mercurial > repos > dfornika > mentalist
changeset 53:2a68ecab8ac0 draft
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit ee2de95921f534b928717e9db75652649d9f60c4-dirty
| author | dfornika |
|---|---|
| date | Wed, 23 May 2018 21:45:50 -0400 |
| parents | 6e77197e134a |
| children | 750c83ff09e5 |
| files | data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py |
| diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py Wed May 23 18:50:11 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py Wed May 23 21:45:50 2018 -0400 @@ -17,13 +17,18 @@ def mentalist_download_enterobase( data_manager_dict, kmer_size, scheme, type, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): + char_to_full_organism_name = { + 'E': 'Escherichia/Shigella', + 'S': 'Salmonella', + 'Y': 'Yersinia' + } translation_table = string.maketrans(string.punctuation, ("_" * 32)) base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_enterobase" today = datetime.date.today().isoformat() scheme_files_path = base_path + "_scheme_" + today database_path = base_path + "_k" + str(kmer_size) + "_" + today database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" - display_name = scheme + " k=" + str(kmer_size) + " (Enterobase) " + today + display_name = char_to_full_organism_name[scheme] + " k=" + str(kmer_size) + " (Enterobase) " + today args = [ 'mentalist', 'download_enterobase', '-s', scheme, '-t', type, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait()