# HG changeset patch
# User estrain
# Date 1653392804 0
# Node ID ba50f77b5db932eb25be10f33d6058c2eb1089f6
# Parent 5ba68abd41f6b5e6290305f8cc79157988ea92d6
Deleted selected files
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py
--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-#!/usr/bin/env python
-# Errol Strain, estrain@gmail.com
-# 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 = 'anonymous@example.com'
-
- 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()
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml
--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-
-
- blast
- hmmer
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Refer to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ for latest database version number.
-
-
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/data_manager_conf.xml
--- a/data_manager_amrfinderplus/data_manager_conf.xml Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-
-
-
-
-
-
-
-
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/test-data/amrfinder_databases.loc
--- a/data_manager_amrfinderplus/test-data/amrfinder_databases.loc Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of amrfinder databases
-#
-# the columns are:
-# value name path
-#
-# for example
-# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/tool-data/amrfinder_databases.loc
--- a/data_manager_amrfinderplus/tool-data/amrfinder_databases.loc Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of amrfinder databases
-#
-# the columns are:
-# value name path
-#
-# for example
-# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/tool_data_table_conf.xml.sample
--- a/data_manager_amrfinderplus/tool_data_table_conf.xml.sample Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
diff -r 5ba68abd41f6 -r ba50f77b5db9 data_manager_amrfinderplus/tool_data_table_conf.xml.test
--- a/data_manager_amrfinderplus/tool_data_table_conf.xml.test Tue May 24 11:46:19 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-