Mercurial > repos > iuc > data_manager_hisat2_index_builder
comparison data_manager/hisat2_index_builder.py @ 0:d3eb4d51b285 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
author | iuc |
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date | Sat, 10 Oct 2015 14:53:43 -0400 |
parents | |
children | b13b84cb11b5 |
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-1:000000000000 | 0:d3eb4d51b285 |
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1 #!/usr/bin/env python | |
2 # Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg | |
3 | |
4 import shlex | |
5 import sys | |
6 import os | |
7 import argparse | |
8 import subprocess | |
9 | |
10 from json import loads, dumps | |
11 | |
12 | |
13 DEFAULT_DATA_TABLE_NAME = "hisat2_indexes" | |
14 | |
15 | |
16 def get_id_name( params, dbkey, fasta_description=None): | |
17 # TODO: ensure sequence_id is unique and does not already appear in location file | |
18 sequence_id = params['param_dict']['sequence_id'] | |
19 if not sequence_id: | |
20 sequence_id = dbkey | |
21 | |
22 sequence_name = params['param_dict']['sequence_name'] | |
23 if not sequence_name: | |
24 sequence_name = fasta_description | |
25 if not sequence_name: | |
26 sequence_name = dbkey | |
27 return sequence_id, sequence_name | |
28 | |
29 | |
30 def build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ): | |
31 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME | |
32 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
33 if not os.path.exists( target_directory ): | |
34 os.mkdir( target_directory ) | |
35 fasta_base_name = os.path.split( options.fasta_filename )[-1] | |
36 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) | |
37 os.symlink( options.fasta_filename, sym_linked_fasta_filename ) | |
38 args = [ 'hisat2-build' ] | |
39 args.extend( shlex.split( options.indexer_options ) ) | |
40 args.extend( [ sym_linked_fasta_filename, sequence_id ] ) | |
41 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) | |
42 return_code = proc.wait() | |
43 if return_code: | |
44 print >> sys.stderr, "Error building index." | |
45 sys.exit( return_code ) | |
46 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) | |
47 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | |
48 | |
49 | |
50 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
51 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
52 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
53 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
54 return data_manager_dict | |
55 | |
56 | |
57 def main(): | |
58 # Parse Command Line | |
59 parser = argparse.ArgumentParser() | |
60 parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) | |
61 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) | |
62 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) | |
63 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) | |
64 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' ) | |
65 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, required=True, default=None ) | |
66 options = parser.parse_args() | |
67 | |
68 filename = options.output | |
69 | |
70 params = loads( open( filename ).read() ) | |
71 data_manager_dict = {} | |
72 | |
73 if options.fasta_dbkey in [ None, '', '?' ]: | |
74 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) | |
75 | |
76 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) | |
77 | |
78 # build the index | |
79 build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ) | |
80 | |
81 # save info to json file | |
82 open( filename, 'wb' ).write( dumps( data_manager_dict ) ) | |
83 | |
84 if __name__ == "__main__": | |
85 main() |