changeset 2:b3585ca01066 draft

Deleted selected files

--- a/fetch_ganon.py	Fri Jul 05 07:56:23 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-#!/usr/bin/env python
-
-import argparse
-import json
-import os
-import os.path
-import sys
-import ftplib
-import socket
-
-def get_refseq_rrna(rrna):
-
-    host = 'ftp.ncbi.nlm.nih.gov'
-    folder_path = 'refseq/TargetedLoci/Bacteria/'
-    file_name="bacteria."+rrna+"rRNA.fna.gz"
-
-    try:
-      f = ftplib.FTP(host)
-    except (socket.error, socket.gaierror) as e:
-      print('ERROR: cannot reach "%s"' % host) 
-      return
-    print('*** Connected to host "%s"' % host)
-
-    try:
-      f.login()
-    except ftplib.error_perm:
-      print('ERROR: cannot login anonymously')
-      f.quit()
-      return
-    print('*** Logged in as "anonymous"')
-
-    try:
-      f.cwd(folder_path)
-    except ftplib.error_perm:
-      print('ERROR: cannot CD to "%s"' % folder_path)
-      f.quit()
-      return
-    print('*** Changed to "%s" folder' % folder_path)
-
-    try:
-      f.retrbinary('RETR %s' % file_name,
-          open(file_name, 'wb').write)
-    except ftplib.error_perm:
-      print('ERROR: cannot read file "%s"' % file_name)
-      os.unlink(file_name)
-    else:
-      print('*** Downloaded "%s" to CWD' % file_name)
-    f.quit()
-
-    return[file_name]
-
-def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name):
-    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
-    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get('ganon_databases', [])
-    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
-    return data_manager_dict
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Download RefSeq rRNA bacterial databases')
-    parser.add_argument('--output_directory', default='/tool-data/ganon', help='Directory to write output to')
-    parser.add_argument('--rrna', help='rRNA sequences to download (5S, 16S, or 23S)')
-    args = parser.parse_args()
-
-    output_directory = args.output_directory
-    if not os.path.exists(output_directory):
-        os.mkdir(output_directory)
-
-    outfile=get_refseq_rrna(args.rrna)
-
-
-    data_manager_dict = {}
-    _add_data_table_entry(data_manager_dict=data_manager_dict,
-      data_table_entry=dict(value="ganon"+args.rrna, dbkey="gannon"+args.rrna, name=args.rrna, path=args.output_directory),
-      data_table_name='ganon_databases')
-    open("output_file", 'w').write(json.dumps(data_manager_dict, sort_keys=True))
-