Mercurial > repos > estrain > data_manager_ganon

comparison data_manager/fetch_ganon.py @ 3:c220590bde7a draft

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author estrain
date Fri, 05 Jul 2019 07:57:02 -0400
parents a50614a513f3
children
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2:b3585ca01066 3:c220590bde7a
14 folder_path = 'refseq/TargetedLoci/Bacteria/' 14 folder_path = 'refseq/TargetedLoci/Bacteria/'
15 file_name="bacteria."+rrna+"rRNA.fna.gz" 15 file_name="bacteria."+rrna+"rRNA.fna.gz"
16 16
17 try: 17 try:
18 f = ftplib.FTP(host) 18 f = ftplib.FTP(host)
19 except (socket.error, socket.gaierror), e: 19 except (socket.error, socket.gaierror) as e:
20 print 'ERROR: cannot reach "%s"' % host 20 print('ERROR: cannot reach "%s"' % host)
21 return 21 return
22 print '*** Connected to host "%s"' % host 22 print('*** Connected to host "%s"' % host)
23 23
24 try: 24 try:
25 f.login() 25 f.login()
26 except ftplib.error_perm: 26 except ftplib.error_perm:
27 print 'ERROR: cannot login anonymously' 27 print('ERROR: cannot login anonymously')
28 f.quit() 28 f.quit()
29 return 29 return
30 print '*** Logged in as "anonymous"' 30 print('*** Logged in as "anonymous"')
31 31
32 try: 32 try:
33 f.cwd(folder_path) 33 f.cwd(folder_path)
34 except ftplib.error_perm: 34 except ftplib.error_perm:
35 print 'ERROR: cannot CD to "%s"' % folder_path 35 print('ERROR: cannot CD to "%s"' % folder_path)
36 f.quit() 36 f.quit()
37 return 37 return
38 print '*** Changed to "%s" folder' % folder_path 38 print('*** Changed to "%s" folder' % folder_path)
39 39
40 try: 40 try:
41 f.retrbinary('RETR %s' % file_name, 41 f.retrbinary('RETR %s' % file_name,
42 open(file_name, 'wb').write) 42 open(file_name, 'wb').write)
43 except ftplib.error_perm: 43 except ftplib.error_perm:
44 print 'ERROR: cannot read file "%s"' % file_name 44 print('ERROR: cannot read file "%s"' % file_name)
45 os.unlink(file_name) 45 os.unlink(file_name)
46 else: 46 else:
47 print '*** Downloaded "%s" to CWD' % file_name 47 print('*** Downloaded "%s" to CWD' % file_name)
48 f.quit() 48 f.quit()
49 49
50 return[file_name] 50 return[file_name]
51 51
52 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name): 52 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name):
68 outfile=get_refseq_rrna(args.rrna) 68 outfile=get_refseq_rrna(args.rrna)
69 69
70 70
71 data_manager_dict = {} 71 data_manager_dict = {}
72 _add_data_table_entry(data_manager_dict=data_manager_dict, 72 _add_data_table_entry(data_manager_dict=data_manager_dict,
73 data_table_entry=dict(value=args.rrna, dbkey=args.rrna, name=args.rrna, path=args.output_directory), 73 data_table_entry=dict(value="ganon"+args.rrna, dbkey="gannon"+args.rrna, name=args.rrna, path=args.output_directory),
74 data_table_name='ganon_databases') 74 data_table_name='ganon_databases')
75 open("output_file", 'w').write(json.dumps(data_manager_dict, sort_keys=True)) 75 open("output_file", 'w').write(json.dumps(data_manager_dict, sort_keys=True))
76 76