# HG changeset patch # User estrain # Date 1562290951 14400 # Node ID a50614a513f30ad22ee69401e4e0003989a9c056 Uploaded diff -r 000000000000 -r a50614a513f3 data_manager/fetch_ganon.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/fetch_ganon.py Thu Jul 04 21:42:31 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), 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=args.rrna, dbkey=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)) + diff -r 000000000000 -r a50614a513f3 data_manager/ganon_data_manager.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/ganon_data_manager.xml Thu Jul 04 21:42:31 2019 -0400 @@ -0,0 +1,29 @@ + + Fetch rRNA data from NCBI RefSeq and create ganon databases + + python + ganon + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r a50614a513f3 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Thu Jul 04 21:42:31 2019 -0400 @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff -r 000000000000 -r a50614a513f3 tool-data/ganon_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ganon_databases.loc.sample Thu Jul 04 21:42:31 2019 -0400 @@ -0,0 +1,8 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - dbkey (database key) +# - path (Name of the ganon DB) +# +#e.g. +#ganon5S5S rRNAdbkey/path/to/ganonDB/5S diff -r 000000000000 -r a50614a513f3 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 04 21:42:31 2019 -0400 @@ -0,0 +1,6 @@ + + + value, name, dbkey, path + +
+