Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison data_manager/salmon_index_builder.py @ 1:c5dea2080109 draft
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author | ieguinoa |
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date | Tue, 14 Aug 2018 11:19:49 -0400 |
parents | |
children | f7d9182bdcab |
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0:6cd60ba8a842 | 1:c5dea2080109 |
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1 #!/usr/bin/env python | |
2 # Based heavily on the kallisto data manager wrapper script by iuc | |
3 from __future__ import print_function | |
4 | |
5 import argparse | |
6 import os | |
7 import subprocess | |
8 import sys | |
9 from json import dumps, loads | |
10 | |
11 DEFAULT_DATA_TABLE_NAME = "salmon_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_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ): | |
29 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME | |
30 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
31 if not os.path.exists( target_directory ): | |
32 os.mkdir( target_directory ) | |
33 if options.kmer_size != '': | |
34 args.append('-k') | |
35 args.append(options.kmer_size) | |
36 args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] ) | |
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=options.fasta_dbkey, name=sequence_name, path=sequence_id ) | |
43 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | |
44 | |
45 | |
46 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
47 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
48 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
49 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
50 return data_manager_dict | |
51 | |
52 | |
53 def main(): | |
54 # Parse Command Line | |
55 parser = argparse.ArgumentParser() | |
56 parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) | |
57 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) | |
58 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) | |
59 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) | |
60 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' ) | |
61 parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' ) | |
62 options = parser.parse_args() | |
63 | |
64 filename = options.output | |
65 | |
66 params = loads( open( filename ).read() ) | |
67 data_manager_dict = {} | |
68 | |
69 if options.fasta_dbkey in [ None, '', '?' ]: | |
70 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) | |
71 | |
72 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) | |
73 | |
74 # build the index | |
75 build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ) | |
76 | |
77 # save info to json file | |
78 open( filename, 'w' ).write( dumps( data_manager_dict ) ) | |
79 | |
80 | |
81 if __name__ == "__main__": | |
82 main() |