annotate data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py @ 0:5ba68abd41f6 draft

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#!/usr/bin/env python
# Errol Strain, [e-mail]
# Database downloads for NCBI AMRFinderPlus

import sys
import os
import tempfile
import shutil
import json
import re
import argparse
from ftplib import FTP


def download_from_ncbi(output_directory):
    NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
    FILENAME = 'version.txt' 
    NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/'
    
    email = '[e-mail]'

    cwd = os.getcwd() 
    os.chdir(output_directory)

    ftp = FTP( NCBI_FTP_SERVER )
    ftp.login( 'anonymous', email)
    ftp.cwd(NCBI_DOWNLOAD_PATH)
    
    #exclude the allele counts folder
    files = ftp.nlst()
    files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)

    for f in files:
      ftp.retrbinary("RETR " + f, open(f, 'wb').write)

    files = ftp.nlst()
    files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
    pointmuts = filter(lambda x: re.search(r'^((?!tab|(?:invokername=tab)).)*$', x), files)
    pointmuts = filter(lambda x: re.search(r'AMR_DNA-', x), pointmuts)


    # Make blast databases
    blastcmd = "makeblastdb -in AMRProt -dbtype prot -logfile /dev/null"
    os.system(blastcmd)
    blastcmd = "makeblastdb -in AMR_CDS -dbtype nucl -logfile /dev/null"
    os.system(blastcmd)

    for f in pointmuts:
      blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null"
      os.system(blastcmd)

    # Make HMM indexes
    hmmcmd="hmmpress -f AMR.LIB > /dev/null 2> /dev/null"
    os.system(hmmcmd)
 
    # Read in version
    with open("version.txt") as f:
      version = f.readline().rstrip()

    ftp.quit()
    
    os.chdir(cwd)    
    
    return version 

def print_json (version,argspath,argsname,argsout):

    data_table_entry = {
      'data_tables' : {
        'amrfinderplus': [
          {
            "value":version,
            "name":argsname,
            "path":argspath,
          }
        ]
      }
    }

    with open(argsout, 'w') as fh:
      json.dump(data_table_entry, fh, indent=2, sort_keys=True)
        
def main():
   
    parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases')
    parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name')
    parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')

    args = parser.parse_args()

    with open(args.out[0]) as fh:
        params = json.load(fh)

    output_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(output_directory)
    data_manager_dict = {}

    #Fetch the files and build blast databases
    version=download_from_ncbi(output_directory)    

    tablename = "AMRFinderPlus Database " + version

    #shutil.copytree("amrdb",args.path[0])
    print_json(version,output_directory,tablename,args.out[0])

if __name__ == "__main__": main()