Mercurial > repos > rnateam > data_manager_bowtie

comparison data_manager/bowtie_index_builder.py @ 0:07578a72b9b2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rnateam
date Tue, 10 Feb 2015 13:35:43 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:07578a72b9b2
1 #!/usr/bin/env python
2
3 import sys
4 import os
5 import tempfile
6 import optparse
7 import subprocess
8
9 from galaxy.util.json import from_json_string, to_json_string
10
11
12 CHUNK_SIZE = 2**20
13
14 DEFAULT_DATA_TABLE_NAME = "bowtie_indexes"
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 def build_bowtie_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space = False ):
30 #TODO: allow multiple FASTA input files
31 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bowtie-index-builder-' )
32 fasta_base_name = os.path.split( fasta_filename )[-1]
33 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
34 os.symlink( fasta_filename, sym_linked_fasta_filename )
35 args = [ 'bowtie-build' ]
36 if color_space:
37 args.append( '-c' )
38 args.append( sym_linked_fasta_filename)
39 args.append( fasta_base_name )
40 args.append( sym_linked_fasta_filename )
41 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bowtie-index-builder-stderr" )
42 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
43 return_code = proc.wait()
44 if return_code:
45 tmp_stderr.flush()
46 tmp_stderr.seek(0)
47 print >> sys.stderr, "Error building index:"
48 while True:
49 chunk = tmp_stderr.read( CHUNK_SIZE )
50 if not chunk:
51 break
52 sys.stderr.write( chunk )
53 sys.exit( return_code )
54 tmp_stderr.close()
55 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
56 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
57
58 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
59 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
60 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
61 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
62 return data_manager_dict
63
64 def main():
65 #Parse Command Line
66 parser = optparse.OptionParser()
67 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
68 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
69 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
70 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
71 parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' )
72 (options, args) = parser.parse_args()
73
74 filename = args[0]
75
76 params = from_json_string( open( filename ).read() )
77 target_directory = params[ 'output_data' ][0]['extra_files_path']
78 os.mkdir( target_directory )
79 data_manager_dict = {}
80
81 dbkey = options.fasta_dbkey
82
83 if dbkey in [ None, '', '?' ]:
84 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
85
86 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
87
88 #build the index
89 build_bowtie_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space )
90
91 #save info to json file
92 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
93
94 if __name__ == "__main__": main()