Mercurial > repos > iuc > data_manager_humann2_database_downloader
diff data_manager/data_manager_humann2_download.py @ 0:048593e41359 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
author | iuc |
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date | Sun, 12 Mar 2017 14:33:34 -0400 |
parents | |
children | 6112a571f012 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_humann2_download.py Sun Mar 12 14:33:34 2017 -0400 @@ -0,0 +1,177 @@ +#!/usr/bin/env python +# +# Data manager for reference data for the 'humann2' Galaxy tools +import datetime +import json +import optparse +import os +import subprocess +import sys + + +HUMANN2_REFERENCE_DATA = { + "full": "Full", + "DEMO": "Demo", + "uniref50_diamond": "Full UniRef50", + "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", + "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", + "uniref90_diamond": "Full UniRef50", + "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", + "DEMO_diamond": "Demo" +} + + +# 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_humann2_db(data_tables, table_name, database, build, target_dir): + """Download HUMAnN2 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 + database: database to download (chocophlan or uniref) + build: build of the database to download + target_dir: directory to put copy or link to the data file + + """ + value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat()) + db_target_dir = os.path.join(target_dir, database) + build_target_dir = os.path.join(db_target_dir, build) + os.makedirs(build_target_dir) + cmd = "humann2_databases --download %s %s %s" % (database, + build, + db_target_dir) + subprocess.check_call(cmd, shell=True) + print(os.listdir(db_target_dir)) + os.rename(os.path.join(db_target_dir, database), build_target_dir) + print(os.listdir(db_target_dir)) + add_data_table_entry( + data_tables, + table_name, + dict( + dbkey=build, + value=value, + name=HUMANN2_REFERENCE_DATA[build], + path=build_target_dir)) + + +if __name__ == "__main__": + print("Starting...") + + # Read command line + parser = optparse.OptionParser(description='Download HUMAnN2 database') + parser.add_option('--database', help="Database name") + parser.add_option('--build', help="Build of the database") + 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() + + if options.database == "chocophlan": + table_name = 'humann2_nucleotide_database' + else: + table_name = 'humann2_protein_database' + add_data_table(data_tables, table_name) + + # Fetch data from specified data sources + download_humann2_db( + data_tables, + table_name, + options.database, + options.build, + target_dir) + + # Write output JSON + print("Outputting JSON") + print(str(json.dumps(data_tables))) + open(jsonfile, 'wb').write(json.dumps(data_tables)) + print("Done.")