Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
diff data_manager/data_manager_metaphlan_download.py @ 6:d8dc037e3c13 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
author | iuc |
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date | Mon, 29 Jul 2024 07:13:31 +0000 |
parents | a88f077f1994 |
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--- a/data_manager/data_manager_metaphlan_download.py Fri Jun 14 21:14:55 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,147 +0,0 @@ -#!/usr/bin/env python -# -# Data manager for reference data for the MetaPhlAn Galaxy tools -import argparse -import json -import subprocess -from datetime import date -from pathlib import Path - - -# Utility functions for interacting with Galaxy JSON -def read_input_json(json_fp): - """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. - - """ - with open(json_fp) as fh: - params = json.load(fh) - return (params['param_dict'], - Path(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(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 = { - '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_metaphlan_db(data_tables, index, table_name, target_dp): - """Download MetaPhlAn 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 - index: version - table_name: name of the table - target_dp: directory to put copy or link to the data file - - """ - db_dp = target_dp / Path(index) - cmd = "metaphlan --install --index %s --bowtie2db %s" % (index, db_dp) - subprocess.check_call(cmd, shell=True) - add_data_table_entry( - data_tables, - table_name, - dict( - dbkey=index, - value='%s-%s' % (index, date.today().strftime("%d%m%Y")), - name="MetaPhlAn clade-specific marker genes (%s)" % index, - path=str(db_dp), - db_version='SGB' if 'SGB' in index else 'legacy')) - - -if __name__ == "__main__": - print("Starting...") - - # Read command line - parser = argparse.ArgumentParser(description='Download and build MetaPhlan database') - parser.add_argument('--index', help="Version of the database") - parser.add_argument('--json', help="Path to JSON file") - args = parser.parse_args() - print("args : %s" % args) - - # Read the input JSON - json_fp = Path(args.json) - params, target_dp = read_input_json(json_fp) - - # Make the target directory - print("Making %s" % target_dp) - target_dp.mkdir(parents=True, exist_ok=True) - - # Set up data tables dictionary - data_tables = create_data_tables_dict() - add_data_table(data_tables, "metaphlan_database_versioned") - - # Fetch data from specified data sources - print("Download and build database") - download_metaphlan_db( - data_tables, - args.index, - "metaphlan_database_versioned", - target_dp) - - # Write output JSON - print("Outputting JSON") - with open(json_fp, 'w') as fh: - json.dump(data_tables, fh, sort_keys=True) - print("Done.")