Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

comparison data_manager/fetch_refseq.py @ 13:dd9f976e9d97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
author sanbi-uwc
date Sat, 08 Sep 2018 03:08:02 -0400
parents 45baee31ca39
children 75c1817c2ecf
comparison
equal deleted inserted replaced
12:45baee31ca39 13:dd9f976e9d97
147 today_str = date.today().strftime('%Y-%m-%d') # ISO 8601 date format 147 today_str = date.today().strftime('%Y-%m-%d') # ISO 8601 date format
148 [release_num, fasta_files] = get_refseq_division(division_name, mol_types, output_directory, args.debug, args.compress) 148 [release_num, fasta_files] = get_refseq_division(division_name, mol_types, output_directory, args.debug, args.compress)
149 if args.galaxy_datamanager_filename is not None: 149 if args.galaxy_datamanager_filename is not None:
150 for i, mol_type in enumerate(mol_types): 150 for i, mol_type in enumerate(mol_types):
151 assert mol_type in fasta_files[i], "Filename does not contain expected mol_type ({}, {})".format(mol_type, fasta_files[i]) 151 assert mol_type in fasta_files[i], "Filename does not contain expected mol_type ({}, {})".format(mol_type, fasta_files[i])
152 unique_key = division_name + '.' + release_num + '.' + mol_type + '.' + today_str 152 unique_key = division_name + '.' + release_num + '.' + mol_type # note: this is now same as dbkey
153 dbkey = division_name + '.' + release_num + '.' + mol_type 153 dbkey = division_name + '.' + release_num + '.' + mol_type
154 desc = 'RefSeq ' + division_name + ' Release ' + release_num + ' ' + mol_type + ' (' + today_str + ')' 154 desc = 'RefSeq ' + division_name + ' Release ' + release_num + ' ' + mol_type + ' (' + today_str + ')'
155 path = os.path.join(output_directory, fasta_files[i]) 155 path = os.path.join(output_directory, fasta_files[i])
156 _add_data_table_entry(data_manager_dict=data_manager_dict, 156 _add_data_table_entry(data_manager_dict=data_manager_dict,
157 data_table_entry=dict(value=unique_key, dbkey=dbkey, name=desc, path=path), 157 data_table_entry=dict(value=unique_key, dbkey=dbkey, name=desc, path=path),