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comparison galaxy_tmap_tool/tmap_wrapper.py @ 10:09951b7d29a4

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Uploaded galaxy_tmap_tool.tar
author greg
date Thu, 21 Jul 2011 09:54:55 -0400
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1 #!/usr/bin/env python
2
3 # TODO
4 # - map1/map2/map3 specific options
5
6 """
7 Runs TMAP on Ion Torrent data.
8 Produces a SAM file containing the mappings.
9 Works with TMAP version 0.0.8 or higher.
10
11 usage: tmap_wrapper.py [options]
12 --threads: The number of threads to use
13 --ref: The reference genome to use or index
14 --fastq: The fastq file to use for the mapping
15 --output: The file to save the output (SAM format)
16 --params: Parameter setting to use (pre_set or full)
17 --fileSource: Whether to use a previously indexed reference sequence or one from history (indexed or history)
18 --matchScore: The match score
19 --mismatchPenalty: Mismatch penalty
20 --gapOpenPenalty: Gap open penalty
21 --gapExtensPenalty: Gap extension penalty
22 --bandWidth: The band width
23 --globalMap: Map the full read (no soft-clipping)
24 --duplicateWindow: Remove duplicate alignments from different algorithms within this bp window (-1 to disable)
25 --scoringThreshold: The score threshold divided by the match score
26 --queueSize: The queue size for the reads
27 --outputFilter: The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)
28 --rgTag: The flag to specify RG tag(s) in the SAM header
29 --rgTagID: The RG ID tag to add to the SAM header
30 --rgTagCN: The RG CN tag to add to the SAM header
31 --rgTagDS: The RG DS tag to add to the SAM header
32 --rgTagDT: The RG DT tag to add to the SAM header
33 --rgTagLB: The RG LB tag to add to the SAM header
34 --rgTagPI: The RG PI tag to add to the SAM header
35 --rgTagPL: The RG PL tag to add to the SAM header
36 --rgTagPU: The RG PU tag to add to the SAM header
37 --rgTagSM: The RG SM tag to add to the SAM header
38 --filterIndependently: Apply the output filter for each algorithm independently
39
40 --map1: Flag to run map1 in the first stage
41 --map1SeedLength: The k-mer length to seed CALs (-1 to disable)
42 --map1SeedMismatches: The maximum number of mismatches in the seed
43 --map1Mismatches: The maximum number of or (read length) fraction of mismatches
44 --map1GapOpens: The maximum number of or (read length) fraction of indel starts
45 --map1GapExtensions: The maximum number of or (read length) fraction of indel extensions
46 --map1MaxCALsDeletion: The maximum number of CALs to extend a deletion
47 --map1EndIndels: Indels are not allowed within this number of bps from the end of the read
48 --map1MaxOptimalCALs: Stop searching when INT optimal CALs have been found
49 --map1MaxNodes: The maximum number of alignment nodes
50
51 --map2: Flag to run map2 in the first stage
52 --map2Coefficient: The coefficient of length-threshold adjustment
53 --map2SeedIntervalSize: The maximum seeding interval size
54 --map2ZBest: Keep the z-best nodes during prefix trie traversal
55 --map2ReverseTrigger: The # seeds to trigger reverse alignment
56
57 --map3: Flag to run map3 in the first stage
58 --map3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)
59 --map3SeedMaxHits: The maximum number of hits returned by a seed
60 --map3SeedWindow: The window of bases in which to group seeds
61 --map3HPEnumeration: The single homopolymer error difference for enumeration
62
63 --MAP1: Flag to run MAP1 in the second stage
64 --MAP1SeedLength: The k-mer length to seed CALs (-1 to disable)
65 --MAP1SeedMismatches: The maximum number of mismatches in the seed
66 --MAP1Mismatches: The maximum number of or (read length) fraction of mismatches
67 --MAP1GapOpens: The maximum number of or (read length) fraction of indel starts
68 --MAP1GapExtensions: The maximum number of or (read length) fraction of indel extensions
69 --MAP1MaxCALsDeletion: The maximum number of CALs to extend a deletion
70 --MAP1EndIndels: Indels are not allowed within this number of bps from the end of the read
71 --MAP1MaxOptimalCALs: Stop searching when INT optimal CALs have been found
72 --MAP1MaxNodes: The maximum number of alignment nodes
73
74 --MAP2: Flag to run MAP2 in the second stage
75 --MAP2Coefficient: The coefficient of length-threshold adjustment
76 --MAP2SeedIntervalSize: The maximum seeding interval size
77 --MAP2ZBest: Keep the z-best nodes during prefix trie traversal
78 --MAP2ReverseTrigger: The # seeds to trigger reverse alignment
79
80 --MAP3: Flag to run MAP3 in the second stage
81 --MAP3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)
82 --MAP3SeedMaxHits: The maximum number of hits returned by a seed
83 --MAP3SeedWindow: The window of bases in which to group seeds
84 --MAP3HPEnumeration: The single homopolymer error difference for enumeration
85
86 --suppressHeader: Suppress header
87 --dbkey: Dbkey for reference genome
88 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
89 """
90
91 import optparse, os, shutil, subprocess, sys, tempfile
92
93 def stop_err( msg ):
94 sys.stderr.write( '%s\n' % msg )
95 sys.exit()
96
97 def map1_parse( map1SeedLength, map1SeedMismatches, map1Mismatches, \
98 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
99 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes ):
100 return '-l %s -s %s -m %s -o %s -e %s -d %s -i %s -b %s -Q %s' % \
101 ( map1SeedLength, map1SeedMismatches, map1Mismatches, \
102 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
103 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes )
104
105 def map2_parse( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger ):
106 return '-c %s -S %s -b %s -N %s' % ( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger )
107
108 def map3_parse( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration ):
109 return '-l %s -S %s -b %s -H %s' % ( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration )
110
111 def __main__():
112 #Parse Command Line
113 parser = optparse.OptionParser()
114 # Global options
115 parser.add_option( '--threads', dest='threads', help='The number of threads to use' )
116 parser.add_option( '--ref', dest='ref', help='The reference genome to use or index' )
117 parser.add_option( '--fastq', dest='fastq', help='The fastq file to use for the mapping' )
118 parser.add_option( '--output', dest='output', help='The file to save the output (SAM format)' )
119 parser.add_option( '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
120 parser.add_option( '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
121 parser.add_option( '--mapall', dest='mapall', help='Flag indicating if mapall options are present')
122 parser.add_option( '--matchScore', dest='matchScore', help='The match score' )
123 parser.add_option( '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
124 parser.add_option( '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
125 parser.add_option( '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
126 parser.add_option( '--bandWidth', dest='bandWidth', help='The band width' )
127 parser.add_option( '--globalMap', dest='globalMap', help='Map the full read (no soft-clipping)' )
128 parser.add_option( '--duplicateWindow', dest='duplicateWindow', help='Remove duplicate alignments from different algorithms within this bp window (-1 to disable)' )
129 parser.add_option( '--scoringThreshold', dest='scoringThreshold', help='The score threshold divided by the match score ' )
130 parser.add_option( '--queueSize', dest='queueSize', help='The queue size for the reads' )
131 parser.add_option( '--outputFilter', dest='outputFilter', help='The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)' )
132 parser.add_option( '--rgTag', dest='rgTag', help='The flag to specify RG tag(s) in the SAM header' )
133 parser.add_option( '--rgTagID', dest='rgTagID', default='', help='The RG ID to add to the SAM header' )
134 parser.add_option( '--rgTagCN', dest='rgTagCN', default='', help='The RG CN to add to the SAM header' )
135 parser.add_option( '--rgTagDS', dest='rgTagDS', default='', help='The RG DS to add to the SAM header' )
136 parser.add_option( '--rgTagDT', dest='rgTagDT', default='', help='The RG DT to add to the SAM header' )
137 parser.add_option( '--rgTagLB', dest='rgTagLB', default='', help='The RG LB to add to the SAM header' )
138 parser.add_option( '--rgTagPI', dest='rgTagPI', default='', help='The RG PI to add to the SAM header' )
139 parser.add_option( '--rgTagPL', dest='rgTagPL', default='', help='The RG PL to add to the SAM header' )
140 parser.add_option( '--rgTagPU', dest='rgTagPU', default='', help='The RG PU to add to the SAM header' )
141 parser.add_option( '--rgTagSM', dest='rgTagSM', default='', help='The RG SM to add to the SAM header' )
142 parser.add_option( '--filterIndependently', dest='filterIndependently', help='Apply the output filter for each algorithm independently' )
143 parser.add_option( '--suppressHeader', dest='suppressHeader', help='Suppress header' )
144 parser.add_option( '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
145 parser.add_option( '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
146 # map 1 - stage 1
147 parser.add_option( '--map1', dest='map1', help='True if map1 should be run in the first stage' )
148 parser.add_option( '--map1SeedLength', dest='map1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
149 parser.add_option( '--map1SeedMismatches', dest='map1SeedMismatches', help='The maximum number of mismatches in the seed ' )
150 parser.add_option( '--map1Mismatches', dest='map1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
151 parser.add_option( '--map1GapOpens', dest='map1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
152 parser.add_option( '--map1GapExtensions', dest='map1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
153 parser.add_option( '--map1MaxCALsDeletion', dest='map1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
154 parser.add_option( '--map1EndIndels', dest='map1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
155 parser.add_option( '--map1MaxOptimalCALs', dest='map1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
156 parser.add_option( '--map1MaxNodes', dest='map1MaxNodes', help='The maximum number of alignment nodes ' )
157 # map 2 - stage 1
158 parser.add_option( '--map2', dest='map2', help='True if map2 should be run in the first stage' )
159 parser.add_option( '--map2Coefficient', dest='map2Coefficient', help='The coefficient of length-threshold adjustment ' )
160 parser.add_option( '--map2SeedIntervalSize', dest='map2SeedIntervalSize', help='The maximum seeding interval size ' )
161 parser.add_option( '--map2ZBest', dest='map2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
162 parser.add_option( '--map2ReverseTrigger', dest='map2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
163 # map 3 - stage 1
164 parser.add_option( '--map3', dest='map3', help='True if map3 should be run in the first stage' )
165 parser.add_option( '--map3SeedLength', dest='map3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
166 parser.add_option( '--map3SeedMaxHits', dest='map3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
167 parser.add_option( '--map3SeedWindow', dest='map3SeedWindow', help='The window of bases in which to group seeds ' )
168 parser.add_option( '--map3HPEnumeration', dest='map3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
169 # map 1 - stage 2
170 parser.add_option( '--MAP1', dest='MAP1', help='True if map1 should be run in the second stage' )
171 parser.add_option( '--MAP1SeedLength', dest='MAP1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
172 parser.add_option( '--MAP1SeedMismatches', dest='MAP1SeedMismatches', help='The maximum number of mismatches in the seed ' )
173 parser.add_option( '--MAP1Mismatches', dest='MAP1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
174 parser.add_option( '--MAP1GapOpens', dest='MAP1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
175 parser.add_option( '--MAP1GapExtensions', dest='MAP1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
176 parser.add_option( '--MAP1MaxCALsDeletion', dest='MAP1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
177 parser.add_option( '--MAP1EndIndels', dest='MAP1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
178 parser.add_option( '--MAP1MaxOptimalCALs', dest='MAP1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
179 parser.add_option( '--MAP1MaxNodes', dest='MAP1MaxNodes', help='The maximum number of alignment nodes ' )
180 # map 2 - stage 2
181 parser.add_option( '--MAP2', dest='MAP2', help='True if map2 should be run in the second stage' )
182 parser.add_option( '--MAP2Coefficient', dest='MAP2Coefficient', help='The coefficient of length-threshold adjustment ' )
183 parser.add_option( '--MAP2SeedIntervalSize', dest='MAP2SeedIntervalSize', help='The maximum seeding interval size ' )
184 parser.add_option( '--MAP2ZBest', dest='MAP2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
185 parser.add_option( '--MAP2ReverseTrigger', dest='MAP2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
186 # map 3 - stage 2
187 parser.add_option( '--MAP3', dest='MAP3', help='True if map3 should be run in the second stage' )
188 parser.add_option( '--MAP3SeedLength', dest='MAP3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
189 parser.add_option( '--MAP3SeedMaxHits', dest='MAP3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
190 parser.add_option( '--MAP3SeedWindow', dest='MAP3SeedWindow', help='The window of bases in which to group seeds ' )
191 parser.add_option( '--MAP3HPEnumeration', dest='MAP3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
192 # parse the options
193 (options, args) = parser.parse_args()
194
195 # output version # of tool
196 try:
197 tmp = tempfile.NamedTemporaryFile().name
198 tmp_stdout = open( tmp, 'wb' )
199 proc = subprocess.Popen( args='tmap 2>&1', shell=True, stdout=tmp_stdout )
200 tmp_stdout.close()
201 returncode = proc.wait()
202 stdout = None
203 for line in open( tmp_stdout.name, 'rb' ):
204 if line.lower().find( 'version' ) >= 0:
205 stdout = line.strip()
206 break
207 if stdout:
208 sys.stdout.write( 'TMAP %s\n' % stdout )
209 else:
210 raise Exception
211 except:
212 sys.stdout.write( 'Could not determine TMAP version\n' )
213
214 fastq = options.fastq
215
216 # make temp directory for placement of indices
217 tmp_index_dir = tempfile.mkdtemp()
218 tmp_dir = tempfile.mkdtemp()
219
220 # index if necessary
221 if options.fileSource == 'history' and not options.do_not_build_index:
222 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
223 ref_file_name = ref_file.name
224 ref_file.close()
225 os.symlink( options.ref, ref_file_name )
226 cmd1 = 'tmap index -f %s -v ' % ( ref_file_name )
227 try:
228 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
229 tmp_stderr = open( tmp, 'wb' )
230 proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
231 returncode = proc.wait()
232 tmp_stderr.close()
233 # get stderr, allowing for case where it's very large
234 tmp_stderr = open( tmp, 'rb' )
235 stderr = ''
236 buffsize = 1048576
237 try:
238 while True:
239 stderr += tmp_stderr.read( buffsize )
240 if not stderr or len( stderr ) % buffsize != 0:
241 break
242 except OverflowError:
243 pass
244 tmp_stderr.close()
245 if returncode != 0:
246 raise Exception, stderr
247 except Exception, e:
248 # clean up temp dirs
249 if os.path.exists( tmp_index_dir ):
250 shutil.rmtree( tmp_index_dir )
251 if os.path.exists( tmp_dir ):
252 shutil.rmtree( tmp_dir )
253 stop_err( 'Error indexing reference sequence. ' + str( e ) )
254 else:
255 ref_file_name = options.ref
256
257 # set up mapping and generate mapping command options
258 if options.params == 'pre_set':
259 mapall_options = '-n %s' % ( options.threads )
260 map1_options = 'map1'
261 map2_options = 'map2'
262 map3_options = 'map3'
263 MAP1_options = ''
264 MAP2_options = ''
265 MAP3_options = ''
266 else:
267 # mapall options
268 if options.globalMap == 'true':
269 globalMap = '-g'
270 else:
271 globalMap = ''
272 if options.rgTag == 'true':
273 rgTag = ''
274 if options.rgTagID != '':
275 rgTag += '-R "ID:' + options.rgTagID + '" '
276 if options.rgTagCN != '':
277 rgTag += '-R "CN:' + options.rgTagCN + '" '
278 if options.rgTagDS != '':
279 rgTag += '-R "DS:' + options.rgTagDS + '" '
280 if options.rgTagDT != '':
281 rgTag += '-R "DT:' + options.rgTagDT + '" '
282 if options.rgTagLB != '':
283 rgTag += '-R "LB:' + options.rgTagLB + '" '
284 if options.rgTagPI != '':
285 rgTag += '-R "PI:' + options.rgTagPI + '" '
286 if options.rgTagPL != '':
287 rgTag += '-R "PL:' + options.rgTagPL + '" '
288 if options.rgTagPU != '':
289 rgTag += '-R "PU:' + options.rgTagPU + '" '
290 if options.rgTagSM != '':
291 rgTag += '-R "SM:' + options.rgTagSM + '" '
292 rgTag.rstrip(' ')
293 else:
294 rgTag = ''
295 if options.filterIndependently == 'true':
296 filterIndependently = '-I'
297 else:
298 filterIndependently = ''
299 if options.mapall == 'true':
300 mapall_options = '-A %s -M %s -O %s -E %s %s -W %s -T %s -q %s -n %s -a %s %s %s' % \
301 ( options.matchScore, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
302 globalMap, options.duplicateWindow, options.scoringThreshold, options.queueSize,
303 options.threads, options.outputFilter, rgTag, filterIndependently )
304 else:
305 mapall_options = ''
306
307 # map1 - stage one
308 if options.map1 == 'true':
309 map1_options = 'map1 %s' % \
310 map1_parse( options.map1SeedLength, options.map1SeedMismatches, options.map1Mismatches, \
311 options.map1GapOpens, options.map1GapExtensions, options.map1MaxCALsDeletion, \
312 options.map1EndIndels, options.map1MaxOptimalCALs, options.map1MaxNodes )
313 else:
314 map1_options = ''
315 # map2 - stage one
316 if options.map2 == 'true':
317 map2_options = 'map2 %s' % \
318 map2_parse( options.map2Coefficient, options.map2SeedIntervalSize, \
319 options.map2ZBest, options.map2ReverseTrigger )
320 else:
321 map2_options = ''
322 # map3 - stage one
323 if options.map3 == 'true':
324 map3_options = 'map3 %s' % \
325 map3_parse( options.map3SeedLength, options.map3SeedMaxHits, \
326 options.map3SeedWindow, options.map3HPEnumeration )
327 else:
328 map3_options = ''
329 # map1 - stage two
330 if options.MAP1== 'true':
331 MAP1_options = 'MAP1 %s' % \
332 map1_parse( options.MAP1SeedLength, options.MAP1SeedMismatches, options.MAP1Mismatches, \
333 options.MAP1GapOpens, options.MAP1GapExtensions, options.MAP1MaxCALsDeletion, \
334 options.MAP1EndIndels, options.MAP1MaxOptimalCALs, options.MAP1MaxNodes )
335 else:
336 MAP1_options = ''
337 # map2 - stage two
338 if options.MAP2 == 'true':
339 MAP2_options = 'MAP2 %s' % \
340 map2_parse( options.MAP2Coefficient, options.MAP2SeedIntervalSize, \
341 options.MAP2ZBest, options.MAP2ReverseTrigger )
342 else:
343 MAP2_options = ''
344 # map3 - stage two
345 if options.MAP3 == 'true':
346 MAP3_options = 'MAP3 %s' % \
347 MAP3_parse( options.MAP3SeedLength, options.MAP3SeedMaxHits, \
348 options.MAP3SeedWindow, options.MAP3HPEnumeration )
349 else:
350 MAP3_options = ''
351
352 #mapping_cmds
353 # prepare actual mapping and generate mapping commands
354 cmd2 = 'tmap mapall -f %s -r %s -F fastq %s -v %s %s %s %s %s %s > %s' % \
355 ( ref_file_name, fastq, mapall_options,
356 map1_options, map2_options, map3_options,
357 MAP1_options, MAP2_options, MAP3_options,
358 options.output )
359 # perform alignments
360 buffsize = 1048576
361 try:
362 # need to nest try-except in try-finally to handle 2.4
363 try:
364 # align
365 try:
366 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
367 tmp_stderr = open( tmp, 'wb' )
368 proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
369 returncode = proc.wait()
370 tmp_stderr.close()
371 # get stderr, allowing for case where it's very large
372 tmp_stderr = open( tmp, 'rb' )
373 stderr = ''
374 try:
375 while True:
376 stderr += tmp_stderr.read( buffsize )
377 if not stderr or len( stderr ) % buffsize != 0:
378 break
379 except OverflowError:
380 pass
381 tmp_stderr.close()
382 if returncode != 0:
383 raise Exception, stderr
384 except Exception, e:
385 raise Exception, 'Error mapping sequence. ' + str( e )
386 # remove header if necessary
387 if options.suppressHeader == 'true':
388 tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
389 tmp_out_name = tmp_out.name
390 tmp_out.close()
391 try:
392 shutil.move( options.output, tmp_out_name )
393 except Exception, e:
394 raise Exception, 'Error moving output file before removing headers. ' + str( e )
395 fout = file( options.output, 'w' )
396 for line in file( tmp_out.name, 'r' ):
397 if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
398 fout.write( line )
399 fout.close()
400 # check that there are results in the output file
401 if os.path.getsize( options.output ) > 0:
402 sys.stdout.write( 'TMAP completed' )
403 else:
404 raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
405 except Exception, e:
406 stop_err( 'The alignment failed.\n' + str( e ) )
407 finally:
408 # clean up temp dir
409 if os.path.exists( tmp_index_dir ):
410 shutil.rmtree( tmp_index_dir )
411 if os.path.exists( tmp_dir ):
412 shutil.rmtree( tmp_dir )
413
414 if __name__=="__main__": __main__()