Mercurial > repos > fubar > data_manager_rnasta
comparison data_manager/rnastar_index_builder.py @ 0:84f6e67cbae5 draft
Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
author | fubar |
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date | Mon, 29 Sep 2014 20:25:10 -0400 |
parents | |
children | ebadd2c92958 |
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-1:000000000000 | 0:84f6e67cbae5 |
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1 #!/usr/bin/env python | |
2 #Dan Blankenberg | |
3 # adapted from Dan's BWA one for rna star | |
4 # ross lazarus sept 2014 | |
5 # | |
6 import sys | |
7 import os | |
8 import tempfile | |
9 import optparse | |
10 import subprocess | |
11 | |
12 from galaxy.util.json import from_json_string, to_json_string | |
13 | |
14 DEFAULT_DATA_TABLE_NAME = "rnastar_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_rnastar_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name, | |
30 sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads): | |
31 #TODO: allow multiple FASTA input files | |
32 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' ) | |
33 fasta_base_name = os.path.split( fasta_filename )[-1] | |
34 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) | |
35 os.symlink( fasta_filename, sym_linked_fasta_filename ) | |
36 pdict={'target_directory':target_directory,'n_threads':n_threads, 'sjdbFileChrStartEnd':sjdbFileChrStartEnd, | |
37 'sjdbGTFtagExonParentTranscript':sjdbGTFtagExonParentTranscript, 'sjdbGTFfeatureExon':sjdbGTFfeatureExon, | |
38 'sjdbGTFchrPrefix':sjdbGTFchrPrefix,'sjdbOverhang':sjdbOverhang, 'sjdbGTFfile':sjdbGTFfile, | |
39 'sym_linked_fasta_filename':sym_linked_fasta_filename} | |
40 | |
41 cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict | |
42 if sjdbGTFfile: | |
43 cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s | |
44 --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict | |
45 elif sjdbFileChrStartEnd: | |
46 cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' | |
47 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" ) | |
48 args = cl.split(' ') | |
49 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) | |
50 return_code = proc.wait() | |
51 if return_code: | |
52 tmp_stderr.flush() | |
53 tmp_stderr.seek(0) | |
54 print >> sys.stderr, "Error building index: retcode=",retcode | |
55 while True: | |
56 chunk = tmp_stderr.read( CHUNK_SIZE ) | |
57 if not chunk: | |
58 break | |
59 sys.stderr.write( chunk ) | |
60 tmp_stderr.close() | |
61 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) | |
62 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | |
63 | |
64 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
65 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
66 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
67 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
68 return data_manager_dict | |
69 | |
70 def main(): | |
71 #Parse Command Line | |
72 parser = optparse.OptionParser() | |
73 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) | |
74 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) | |
75 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) | |
76 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) | |
77 parser.add_option( '--out_file', default=None) | |
78 parser.add_option( '--out_index_path', default=None) | |
79 parser.add_option( '--sjdbGTFfile', type="string", default=None ) | |
80 parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None ) | |
81 parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None ) | |
82 parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None ) | |
83 parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None ) | |
84 parser.add_option( '--sjdbOverhang', type="int", default=100 ) | |
85 parser.add_option( '--runThreadN', type="int", default=4 ) | |
86 (options, args) = parser.parse_args() | |
87 | |
88 filename = options.out_file | |
89 params = from_json_string( open( filename ).read() ) | |
90 target_directory = options.out_index_path | |
91 os.mkdir( target_directory ) | |
92 data_manager_dict = {} | |
93 | |
94 dbkey = options.fasta_dbkey | |
95 | |
96 if dbkey in [ None, '', '?' ]: | |
97 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) | |
98 | |
99 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) | |
100 | |
101 #build the index | |
102 build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name, | |
103 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile, | |
104 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, | |
105 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, | |
106 n_threads=options.runThreadN ) | |
107 | |
108 #save info to json file | |
109 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) | |
110 | |
111 if __name__ == "__main__": main() |