changeset 1:9de84cd78a82 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_ganon.py	Fri Jul 05 07:56:23 2019 -0400
@@ -0,0 +1,76 @@
+#!/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))
+