Mercurial > repos > devteam > data_manager_sam_fasta_index_builder

comparison data_manager/data_manager_sam_fasta_index_builder.py @ 3:1f54e98616af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:13:56 -0400
parents 2a1ac1abc3f7
children cc4ef4d38cf9
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2:2a1ac1abc3f7 3:1f54e98616af
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 #Dan Blankenberg 2 # Dan Blankenberg
3 3
4 import json 4 import json
5 import optparse 5 import optparse
6 import os 6 import os
7 import subprocess 7 import subprocess
10 10
11 CHUNK_SIZE = 2**20 11 CHUNK_SIZE = 2**20
12 12
13 DEFAULT_DATA_TABLE_NAME = "fasta_indexes" 13 DEFAULT_DATA_TABLE_NAME = "fasta_indexes"
14 14
15
15 def get_id_name( params, dbkey, fasta_description=None): 16 def get_id_name( params, dbkey, fasta_description=None):
16 #TODO: ensure sequence_id is unique and does not already appear in location file 17 # TODO: ensure sequence_id is unique and does not already appear in location file
17 sequence_id = params['param_dict']['sequence_id'] 18 sequence_id = params['param_dict']['sequence_id']
18 if not sequence_id: 19 if not sequence_id:
19 sequence_id = dbkey 20 sequence_id = dbkey
20 21
21 sequence_name = params['param_dict']['sequence_name'] 22 sequence_name = params['param_dict']['sequence_name']
22 if not sequence_name: 23 if not sequence_name:
23 sequence_name = fasta_description 24 sequence_name = fasta_description
24 if not sequence_name: 25 if not sequence_name:
25 sequence_name = dbkey 26 sequence_name = dbkey
26 return sequence_id, sequence_name 27 return sequence_id, sequence_name
27 28
29
28 def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): 30 def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
29 #TODO: allow multiple FASTA input files 31 # TODO: allow multiple FASTA input files
30 assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename 32 assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename
31 fasta_base_name = os.path.split( fasta_filename )[-1] 33 fasta_base_name = os.path.split( fasta_filename )[-1]
32 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) 34 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
33 os.symlink( fasta_filename, sym_linked_fasta_filename ) 35 os.symlink( fasta_filename, sym_linked_fasta_filename )
34 36
35 args = [ 'samtools', 'faidx' ] 37 args = [ 'samtools', 'faidx' ]
36 args.append( sym_linked_fasta_filename ) 38 args.append( sym_linked_fasta_filename )
37 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" ) 39 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-sam_fa_index_builder-stderr")
38 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) 40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
39 return_code = proc.wait() 41 return_code = proc.wait()
40 if return_code: 42 if return_code:
41 tmp_stderr.flush() 43 tmp_stderr.flush()
42 tmp_stderr.seek( 0 ) 44 tmp_stderr.seek( 0 )
49 sys.exit( return_code ) 51 sys.exit( return_code )
50 tmp_stderr.close() 52 tmp_stderr.close()
51 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) 53 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
52 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) 54 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
53 55
56
54 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 57 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
55 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 58 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
56 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) 59 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
57 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) 60 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
58 return data_manager_dict 61 return data_manager_dict
59 62
63
60 def main(): 64 def main():
61 #Parse Command Line
62 parser = optparse.OptionParser() 65 parser = optparse.OptionParser()
63 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) 66 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
64 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) 67 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
65 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) 68 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
66 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) 69 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
67 (options, args) = parser.parse_args() 70 (options, args) = parser.parse_args()
68 71
69 filename = args[0] 72 filename = args[0]
70 73
71 params = json.loads( open( filename ).read() ) 74 params = json.loads( open( filename ).read() )
72 target_directory = params[ 'output_data' ][0]['extra_files_path'] 75 target_directory = params[ 'output_data' ][0]['extra_files_path']
73 os.mkdir( target_directory ) 76 os.mkdir( target_directory )
74 data_manager_dict = {} 77 data_manager_dict = {}
75 78
76 if options.fasta_dbkey in [ None, '', '?' ]: 79 if options.fasta_dbkey in [ None, '', '?' ]:
77 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) 80 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
78 81
79 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) 82 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
80 83
81 #build the index 84 # build the index
82 build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) 85 build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
83 86
84 #save info to json file 87 # save info to json file
85 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) 88 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
86 89
87 if __name__ == "__main__": main() 90
91 if __name__ == "__main__":
92 main()