Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

comparison data_manager/fetch_refseq.py @ 12:45baee31ca39 draft

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planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
author sanbi-uwc
date Fri, 07 Sep 2018 20:14:04 -0400
parents b1e8f8a613e6
children dd9f976e9d97
comparison
equal deleted inserted replaced
11:b1e8f8a613e6 12:45baee31ca39
145 today_str = args.pin_date 145 today_str = args.pin_date
146 else: 146 else:
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(args.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 + '.' + today_str
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])