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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import json
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5 import os
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6 import os.path
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7 import sys
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8 import ftplib
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9 import socket
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10
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11 def get_refseq_rrna(rrna):
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12
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13 host = 'ftp.ncbi.nlm.nih.gov'
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14 folder_path = 'refseq/TargetedLoci/Bacteria/'
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15 file_name="bacteria."+rrna+"rRNA.fna.gz"
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16
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17 try:
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18 f = ftplib.FTP(host)
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19 except (socket.error, socket.gaierror), e:
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20 print 'ERROR: cannot reach "%s"' % host
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21 return
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22 print '*** Connected to host "%s"' % host
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23
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24 try:
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25 f.login()
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26 except ftplib.error_perm:
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27 print 'ERROR: cannot login anonymously'
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28 f.quit()
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29 return
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30 print '*** Logged in as "anonymous"'
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31
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32 try:
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33 f.cwd(folder_path)
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34 except ftplib.error_perm:
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35 print 'ERROR: cannot CD to "%s"' % folder_path
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36 f.quit()
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37 return
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38 print '*** Changed to "%s" folder' % folder_path
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39
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40 try:
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41 f.retrbinary('RETR %s' % file_name,
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42 open(file_name, 'wb').write)
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43 except ftplib.error_perm:
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44 print 'ERROR: cannot read file "%s"' % file_name
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45 os.unlink(file_name)
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46 else:
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47 print '*** Downloaded "%s" to CWD' % file_name
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48 f.quit()
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49
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50 return[file_name]
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51
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52 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name):
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53 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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54 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get('ganon_databases', [])
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55 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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56 return data_manager_dict
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57
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58 if __name__ == '__main__':
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59 parser = argparse.ArgumentParser(description='Download RefSeq rRNA bacterial databases')
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60 parser.add_argument('--output_directory', default='/tool-data/ganon', help='Directory to write output to')
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61 parser.add_argument('--rrna', help='rRNA sequences to download (5S, 16S, or 23S)')
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62 args = parser.parse_args()
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63
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64 output_directory = args.output_directory
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65 if not os.path.exists(output_directory):
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66 os.mkdir(output_directory)
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67
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68 outfile=get_refseq_rrna(args.rrna)
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69
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70
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71 data_manager_dict = {}
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72 _add_data_table_entry(data_manager_dict=data_manager_dict,
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73 data_table_entry=dict(value=args.rrna, dbkey=args.rrna, name=args.rrna, path=args.output_directory),
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74 data_table_name='ganon_databases')
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75 open("output_file", 'w').write(json.dumps(data_manager_dict, sort_keys=True))
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76
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