Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
view data_manager/novocraft_index_builder.py @ 10:68b7023c6a2f draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 41c23255d958406b015574dd15b07d44175a2c1b
author | sanbi-uwc |
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date | Sat, 05 Mar 2016 10:29:02 -0500 |
parents | 56e8324519c4 |
children | a9b725202132 |
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#!/usr/bin/env python # Z. Mashologu (SANBI-UWC) # import dict as dict from __future__ import print_function import os import sys import urllib2 import logging import argparse import shlex from subprocess import check_call, CalledProcessError log = logging.getLogger(__name__) from json import loads, dumps DEFAULT_DATA_TABLE_NAME = "novocraft_index" def get_dbkey_id_name(params, dbkey_description=None): dbkey = params['param_dict']['dbkey'] # TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: sequence_id = dbkey # uuid.uuid4() generate and use an uuid instead? sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = dbkey_description if not sequence_name: sequence_name = dbkey return dbkey, sequence_id, sequence_name def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME): if os.path.exists(target_directory) and not os.path.isdir(target_directory): print("Output directory path already exists but is not a directory: {}".format(target_directory), file=sys.stderr) elif not os.path.exists(target_directory): os.mkdir(target_directory) if 'GALAXY_SLOTS' in os.environ: nslots = os.environ['GALAXY_SLOTS'] else: nslots = 1 #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( # target_directory, # fasta_filename, # nslots) #cmdline = shlex.split(cmdline_str) index_filename = 'foo' cmdline = ('touch', '{}/{}'.format(target_directory, index_filename)) try: check_call(cmdline) except CalledProcessError: print("Error building RNA STAR index", file=sys.stderr) data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.join(target_directory, index_filename) ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) return ( index_filename ) def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 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( data_table_name, [] ) data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) return data_manager_dict def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): # TODO: we should automatically do decompression here urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n'))) fasta_reader = [urllib2.urlopen(url) for url in urls] _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, dbkey, sequence_id, sequence_name, data_table_name) def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): # TODO: allow multiple FASTA input files input_filename = params['param_dict']['reference_source']['input_fasta'] _make_novocraft_index(data_manager_dict, input_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name) REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history) def main(): parser = argparse.ArgumentParser(description="Generate Novo-craft genome index and JSON describing this") parser.add_argument('output_filename') parser.add_argument('--dbkey_description') parser.add_argument('--data_table_name', default='novocraft_index') args = parser.parse_args() filename = args.output_filename params = loads(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path'] os.makedirs(target_directory) data_manager_dict = {} dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) if dbkey in [None, '', '?']: raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) # Fetch the FASTA REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\ (data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME) open(filename, 'wb').write(dumps( data_manager_dict )) if __name__ == "__main__": main()