Mercurial > repos > sanbi-uwc > data_manager_fetch_artic_primers

comparison data_manager/fetch_artic_primers.py @ 1:59b3556d9ec8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
author sanbi-uwc
date Thu, 16 Apr 2020 20:45:35 +0000
parents c401f63b3d12
children 6114f017f819
comparison
equal deleted inserted replaced
0:c401f63b3d12 1:59b3556d9ec8
17 'ARTICv2': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed', 17 'ARTICv2': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed',
18 'ARTICv3': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed' 18 'ARTICv3': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed'
19 } 19 }
20 20
21 if not os.path.isdir(output_directory): 21 if not os.path.isdir(output_directory):
22 os.makedirs(output_directory) 22 os.makedirs(output_directory)
23 data_manager_dict = json.load(open(output_filename)) 23 data_manager_dict = {}
24 data_manager_dict['data_tables'] = json.load(open(output_filename)).get('data_tables', {})
24 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) 25 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
25 data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, []) 26 data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, [])
26 27
27 data = [] 28 data = []
28 for name, url in primer_sets.items(): 29 for name, url in primer_sets.items():
30 if name not in primers:
31 continue
29 response = requests.get(url) 32 response = requests.get(url)
30 if response.status_code != 200: 33 if response.status_code != 200:
31 print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr) 34 print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
32 exit(response.status_code) 35 exit(response.status_code)
33 bed_output_filename = os.path.join(output_directory, name + '.bed') 36 bed_output_filename = os.path.join(output_directory, name + '.bed')