Mercurial > repos > iuc > data_manager_metaphlan2_database_downloader
diff data_manager/data_manager_metaphlan2_download.py @ 0:9c4ad82be5bd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
author | iuc |
---|---|
date | Sat, 04 Mar 2017 12:11:20 -0500 |
parents | |
children | 83f07f40b200 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_metaphlan2_download.py Sat Mar 04 12:11:20 2017 -0500 @@ -0,0 +1,150 @@ +#!/usr/bin/env python +# +# Data manager for reference data for the 'humann2' Galaxy tools +import json +import optparse +import os +import subprocess +import sys + + +# Utility functions for interacting with Galaxy JSON +def read_input_json(jsonfile): + """Read the JSON supplied from the data manager tool + + Returns a tuple (param_dict,extra_files_path) + + 'param_dict' is an arbitrary dictionary of parameters + input into the tool; 'extra_files_path' is the path + to a directory where output files must be put for the + receiving data manager to pick them up. + + NB the directory pointed to by 'extra_files_path' + doesn't exist initially, it is the job of the script + to create it if necessary. + + """ + params = json.loads(open(jsonfile).read()) + return (params['param_dict'], + params['output_data'][0]['extra_files_path']) + + +# Utility functions for creating data table dictionaries +# +# Example usage: +# >>> d = create_data_tables_dict() +# >>> add_data_table(d,'my_data') +# >>> add_data_table_entry(dict(dbkey='hg19',value='human')) +# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) +# >>> print str(json.dumps(d)) +def create_data_tables_dict(): + """Return a dictionary for storing data table information + + Returns a dictionary that can be used with 'add_data_table' + and 'add_data_table_entry' to store information about a + data table. It can be converted to JSON to be sent back to + the data manager. + + """ + d = {} + d['data_tables'] = {} + return d + + +def add_data_table(d, table): + """Add a data table to the data tables dictionary + + Creates a placeholder for a data table called 'table'. + + """ + d['data_tables'][table] = [] + + +def add_data_table_entry(d, table, entry): + """Add an entry to a data table + + Appends an entry to the data table 'table'. 'entry' + should be a dictionary where the keys are the names of + columns in the data table. + + Raises an exception if the named data table doesn't + exist. + + """ + try: + d['data_tables'][table].append(entry) + except KeyError: + raise Exception("add_data_table_entry: no table '%s'" % table) + + +def download_metaphlan2_db(data_tables, build, table_name, target_dir): + """Download MetaPhlAn2 database + + Creates references to the specified file(s) on the Galaxy + server in the appropriate data table (determined from the + file extension). + + The 'data_tables' dictionary should have been created using + the 'create_data_tables_dict' and 'add_data_table' functions. + + Arguments: + data_tables: a dictionary containing the data table info + table_name: name of the table + target_dir: directory to put copy or link to the data file + + """ + cmd = "download_metaphlan2_db.py --output %s" % (target_dir) + db_dir = os.path.join(target_dir, build) + subprocess.check_call(cmd, shell=True) + os.rename(os.path.join(target_dir, "db_v20"), db_dir) + add_data_table_entry( + data_tables, + table_name, + dict( + dbkey=build, + value="mpa_v20_m200", + name="MetaPhlAn2 clade-specific marker genes", + path=db_dir)) + + +if __name__ == "__main__": + print("Starting...") + + # Read command line + parser = optparse.OptionParser(description='Download MetaPhlan2 database') + parser.add_option('--database', help="Database name") + options, args = parser.parse_args() + print("args : %s" % args) + + # Check for JSON file + if len(args) != 1: + sys.stderr.write("Need to supply JSON file name") + sys.exit(1) + + jsonfile = args[0] + + # Read the input JSON + params, target_dir = read_input_json(jsonfile) + + # Make the target directory + print("Making %s" % target_dir) + os.mkdir(target_dir) + + # Set up data tables dictionary + data_tables = create_data_tables_dict() + add_data_table(data_tables, "metaphlan2_database") + + # Fetch data from specified data sources + if options.database == "db_v20": + download_metaphlan2_db( + data_tables, + "v20", + "metaphlan2_database", + target_dir) + + # Write output JSON + print("Outputting JSON") + print(str(json.dumps(data_tables))) + with open(jsonfile, 'wb') as out: + out.write(json.dumps(data_tables)) + print("Done.")