Mercurial > repos > iuc > data_manager_humann2_database_downloader
view data_manager/data_manager_humann2_download.py @ 2:6112a571f012 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit f474a24a52dcda7fb6681869e24f566d28f1e457
author | iuc |
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date | Fri, 23 Jun 2017 06:00:47 -0400 |
parents | 048593e41359 |
children | 9244804f69a7 |
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#!/usr/bin/env python # # Data manager for reference data for the 'humann2' Galaxy tools import datetime import json import optparse import os import shutil 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 UniRef90", "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 --update-config no" % ( database, build, db_target_dir) subprocess.check_call(cmd, shell=True) shutil.move(os.path.join(db_target_dir, database), build_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.")