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1 #!/usr/bin/env python
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2 # Errol Strain, estrain@gmail.com
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3 # Database downloads for NCBI AMRFinderPlus
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4
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5 import sys
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6 import os
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7 import tempfile
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8 import shutil
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9 import json
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10 import re
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11 import argparse
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12 from ftplib import FTP
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13
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14
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5
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15 def download_from_ncbi(output_directory):
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16 NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
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17 FILENAME = 'version.txt'
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18 NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/'
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19
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20 email = 'anonymous@example.com'
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21
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22 cwd = os.getcwd()
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23 os.chdir(output_directory)
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24
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25 ftp = FTP( NCBI_FTP_SERVER )
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26 ftp.login( 'anonymous', email)
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27 ftp.cwd(NCBI_DOWNLOAD_PATH)
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28
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29 #exclude the allele counts folder
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30 files = ftp.nlst()
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31 files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
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32
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33 for f in files:
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34 ftp.retrbinary("RETR " + f, open(f, 'wb').write)
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35
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36 files = ftp.nlst()
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37 files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
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38 pointmuts = filter(lambda x: re.search(r'^((?!tab|(?:invokername=tab)).)*$', x), files)
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39 pointmuts = filter(lambda x: re.search(r'AMR_DNA-', x), pointmuts)
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40
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41
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42 # Make blast databases
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43 blastcmd = "makeblastdb -in AMRProt -dbtype prot -logfile /dev/null"
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44 os.system(blastcmd)
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45 blastcmd = "makeblastdb -in AMR_CDS -dbtype nucl -logfile /dev/null"
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46 os.system(blastcmd)
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47
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48 for f in pointmuts:
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49 blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null"
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50 os.system(blastcmd)
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51
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52 # Make HMM indexes
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53 hmmcmd="hmmpress -f AMR.LIB > /dev/null 2> /dev/null"
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54 os.system(hmmcmd)
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55
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56 # Read in version
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57 with open("version.txt") as f:
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58 version = f.readline().rstrip()
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59
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60 ftp.quit()
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61
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62 os.chdir(cwd)
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63
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64 return version
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65
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66 def print_json (version,argspath,argsname,argsout):
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67
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68 data_table_entry = {
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69 'data_tables' : {
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70 'amrfinderplus': [
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71 {
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72 "value":version,
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73 "name":argsname,
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74 "path":argspath,
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75 }
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76 ]
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77 }
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78 }
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79
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80 with open(argsout, 'w') as fh:
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81 json.dump(data_table_entry, fh, indent=2, sort_keys=True)
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82
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83 def main():
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84
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85 parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases')
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86 parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name')
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87 parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
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88
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89 args = parser.parse_args()
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90
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91 with open(args.out[0]) as fh:
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92 params = json.load(fh)
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93
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94 output_directory = params['output_data'][0]['extra_files_path']
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95 os.mkdir(output_directory)
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96 data_manager_dict = {}
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97
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98 #Fetch the files and build blast databases
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99 version=download_from_ncbi(output_directory)
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100
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101 tablename = "AMRFinderPlus Database " + version
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102
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103 #shutil.copytree("amrdb",args.path[0])
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104 print_json(version,output_directory,tablename,args.out[0])
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105
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106 if __name__ == "__main__": main()
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