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comparison data_manager/bowtie2_index_builder.py @ 0:68fd790f3916 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
author matthias
date Thu, 02 Apr 2020 13:16:53 +0000
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-1:000000000000 0:68fd790f3916
1 #!/usr/bin/env python
2 # Dan Blankenberg
3 from __future__ import print_function
4
5 import optparse
6 import os
7 import subprocess
8 import sys
9 from json import dumps, loads
10
11 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]
12
13
14 def get_id_name(params, dbkey, fasta_description=None):
15 # TODO: ensure sequence_id is unique and does not already appear in location file
16 sequence_id = params['param_dict']['sequence_id']
17 if not sequence_id:
18 sequence_id = dbkey
19
20 sequence_name = params['param_dict']['sequence_name']
21 if not sequence_name:
22 sequence_name = fasta_description
23 if not sequence_name:
24 sequence_name = dbkey
25 return sequence_id, sequence_name
26
27
28 def build_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
29 # TODO: allow multiple FASTA input files
30 fasta_base_name = os.path.split(fasta_filename)[-1]
31 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
32 os.symlink(fasta_filename, sym_linked_fasta_filename)
33 args = ['bowtie2-build', sym_linked_fasta_filename, sequence_id]
34 threads = os.environ.get('GALAXY_SLOTS')
35 if threads:
36 args.extend(['--threads', threads])
37 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
38 return_code = proc.wait()
39 if return_code:
40 print("Error building index.", file=sys.stderr)
41 sys.exit(return_code)
42 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
43 for data_table_name in data_table_names:
44 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
45
46
47 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
48 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
49 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
50 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
51 return data_manager_dict
52
53
54 def main():
55 parser = optparse.OptionParser()
56 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
57 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
58 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
59 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name')
60 (options, args) = parser.parse_args()
61
62 filename = args[0]
63
64 params = loads(open(filename).read())
65 target_directory = params['output_data'][0]['extra_files_path']
66 os.mkdir(target_directory)
67 data_manager_dict = {}
68
69 dbkey = options.fasta_dbkey
70
71 if dbkey in [None, '', '?']:
72 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
73
74 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
75
76 # build the index
77 build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
78
79 # save info to json file
80 with open(filename, 'w') as json_out:
81 json_out.write(dumps(data_manager_dict, sort_keys=True))
82
83
84 if __name__ == "__main__":
85 main()