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comparison tools/sr_mapping/bfast_wrapper.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env python
2
3 """
4 Runs BFAST on single-end or paired-end data.
5 TODO: more documentation
6
7 TODO:
8 - auto-detect gzip or bz2
9 - split options (?)
10 - queue lengths (?)
11 - assumes reference always has been indexed
12 - main and secondary indexes
13 - scoring matrix file ?
14 - read group file ?
15
16 usage: bfast_wrapper.py [options]
17 -r, --ref=r: The reference genome to use or index
18 -f, --fastq=f: The fastq file to use for the mapping
19 -F, --output=u: The file to save the output (SAM format)
20 -s, --fileSource=s: Whether to use a previously indexed reference sequence or one from history (indexed or history)
21 -p, --params=p: Parameter setting to use (pre_set or full)
22 -n, --numThreads=n: The number of threads to use
23 -A, --space=A: The encoding space (0: base 1: color)
24 -o, --offsets=o: The offsets for 'match'
25 -l, --loadAllIndexes=l: Load all indexes into memory
26 -k, --keySize=k: truncate key size in 'match'
27 -K, --maxKeyMatches=K: the maximum number of matches to allow before a key is ignored
28 -M, --maxNumMatches=M: the maximum number of matches to allow before the read is discarded
29 -w, --whichStrand=w: the strands to consider (0: both 1: forward 2: reverse)
30 -t, --timing=t: output timing information to stderr
31 -u, --ungapped=u: performed ungapped local alignment
32 -U, --unconstrained=U: performed local alignment without mask constraints
33 -O, --offset=O: the number of bases before and after each hit to consider in local alignment
34 -q, --avgMismatchQuality=q: average mismatch quality
35 -a, --algorithm=a: post processing algorithm (0: no filtering, 1: all passing filters, 2: unique, 3: best scoring unique, 4: best score all)
36 -P, --disallowPairing=P: do not choose alignments based on pairing
37 -R, --reverse=R: paired end reads are given on reverse strands
38 -z, --random=z: output a random best scoring alignment
39 -D, --dbkey=D: Dbkey for reference genome
40 -H, --suppressHeader=H: Suppress the sam header
41 """
42
43 import optparse, os, shutil, subprocess, sys, tempfile
44
45 def stop_err( msg ):
46 sys.stderr.write( '%s\n' % msg )
47 sys.exit()
48
49 def __main__():
50 #Parse Command Line
51 parser = optparse.OptionParser()
52 parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' )
53 parser.add_option( '-f', '--fastq', dest='fastq', help='The fastq file to use for the mapping' )
54 parser.add_option( '-F', '--output', dest='output', help='The file to save the output (SAM format)' )
55 parser.add_option( '-A', '--space', dest='space', type="choice", default='0', choices=('0','1' ), help='The encoding space (0: base 1: color)' )
56 parser.add_option( '-H', '--suppressHeader', action="store_true", dest='suppressHeader', default=False, help='Suppress header' )
57 parser.add_option( '-n', '--numThreads', dest='numThreads', type="int", default="1", help='The number of threads to use' )
58 parser.add_option( '-t', '--timing', action="store_true", default=False, dest='timing', help='output timming information to stderr' )
59 parser.add_option( '-l', '--loadAllIndexes', action="store_true", default=False, dest='loadAllIndexes', help='Load all indexes into memory' )
60 parser.add_option( '-m', '--indexMask', dest='indexMask', help='String containing info on how to build custom indexes' )
61 parser.add_option( "-b", "--buildIndex", action="store_true", dest="buildIndex", default=False, help='String containing info on how to build custom indexes' )
62 parser.add_option( "--indexRepeatMasker", action="store_true", dest="indexRepeatMasker", default=False, help='Do not index lower case sequences. Such as those created by RepeatMasker' )
63 parser.add_option( '--indexContigOptions', dest='indexContigOptions', default="", help='The contig range options to use for the indexing' )
64 parser.add_option( '--indexExonsFileName', dest='indexExonsFileName', default="", help='The exons file to use for the indexing' )
65
66 parser.add_option( '-o', '--offsets', dest='offsets', default="", help='The offsets for \'match\'' )
67 parser.add_option( '-k', '--keySize', dest='keySize', type="int", default="-1", help='truncate key size in \'match\'' )
68 parser.add_option( '-K', '--maxKeyMatches', dest='maxKeyMatches', type="int", default="-1", help='the maximum number of matches to allow before a key is ignored' )
69 parser.add_option( '-M', '--maxNumMatches', dest='maxNumMatches', type="int", default="-1", help='the maximum number of matches to allow bfore the read is discarded' )
70 parser.add_option( '-w', '--whichStrand', dest='whichStrand', type="choice", default='0', choices=('0','1','2'), help='the strands to consider (0: both 1: forward 2: reverse)' )
71
72 parser.add_option( '--scoringMatrixFileName', dest='scoringMatrixFileName', help='Scoring Matrix file used to score the alignments' )
73 parser.add_option( '-u', '--ungapped', dest='ungapped', action="store_true", default=False, help='performed ungapped local alignment' )
74 parser.add_option( '-U', '--unconstrained', dest='unconstrained', action="store_true", default=False, help='performed local alignment without mask constraints' )
75 parser.add_option( '-O', '--offset', dest='offset', type="int", default="0", help='the number of bases before and after each hit to consider in local alignment' )
76 parser.add_option( '-q', '--avgMismatchQuality', type="int", default="-1", dest='avgMismatchQuality', help='average mismatch quality' )
77
78 parser.add_option( '-a', '--algorithm', dest='algorithm', default='0', type="choice", choices=('0','1','2','3','4' ), help='post processing algorithm (0: no filtering, 1: all passing filters, 2: unique, 3: best scoring unique, 4: best score all' )
79 parser.add_option( '--unpaired', dest='unpaired', action="store_true", default=False, help='do not choose alignments based on pairing' )
80 parser.add_option( '--reverseStrand', dest='reverseStrand', action="store_true", default=False, help='paired end reads are given on reverse strands' )
81 parser.add_option( '--pairedEndInfer', dest='pairedEndInfer', action="store_true", default=False, help='break ties when one end of a paired end read by estimating the insert size distribution' )
82 parser.add_option( '--randomBest', dest='randomBest', action="store_true", default=False, help='output a random best scoring alignment' )
83
84 (options, args) = parser.parse_args()
85
86 # output version # of tool
87 try:
88 tmp = tempfile.NamedTemporaryFile().name
89 tmp_stdout = open( tmp, 'wb' )
90 proc = subprocess.Popen( args='bfast 2>&1', shell=True, stdout=tmp_stdout )
91 tmp_stdout.close()
92 returncode = proc.wait()
93 stdout = None
94 for line in open( tmp_stdout.name, 'rb' ):
95 if line.lower().find( 'version' ) >= 0:
96 stdout = line.strip()
97 break
98 if stdout:
99 sys.stdout.write( '%s\n' % stdout )
100 else:
101 raise Exception
102 except:
103 sys.stdout.write( 'Could not determine BFAST version\n' )
104
105 buffsize = 1048576
106
107 # make temp directory for bfast, requires trailing slash
108 tmp_dir = '%s/' % tempfile.mkdtemp()
109
110 #'generic' options used in all bfast commands here
111 if options.timing:
112 all_cmd_options = "-t"
113 else:
114 all_cmd_options = ""
115
116 try:
117 if options.buildIndex:
118 reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' ).name
119 #build bfast indexes
120 os.symlink( options.ref, reference_filepath )
121
122 #bfast fast2brg
123 try:
124 nuc_space = [ "0" ]
125 if options.space == "1":
126 #color space localalign appears to require nuc space brg
127 nuc_space.append( "1" )
128 for space in nuc_space:
129 cmd = 'bfast fasta2brg -f "%s" -A "%s" %s' % ( reference_filepath, space, all_cmd_options )
130 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
131 tmp_stderr = open( tmp, 'wb' )
132 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
133 returncode = proc.wait()
134 tmp_stderr.close()
135 # get stderr, allowing for case where it's very large
136 tmp_stderr = open( tmp, 'rb' )
137 stderr = ''
138 try:
139 while True:
140 stderr += tmp_stderr.read( buffsize )
141 if not stderr or len( stderr ) % buffsize != 0:
142 break
143 except OverflowError:
144 pass
145 tmp_stderr.close()
146 if returncode != 0:
147 raise Exception, stderr
148 except Exception, e:
149 raise Exception, 'Error in \'bfast fasta2brg\'.\n' + str( e )
150
151 #bfast index
152 try:
153 all_index_cmds = 'bfast index %s -f "%s" -A "%s" -n "%s"' % ( all_cmd_options, reference_filepath, options.space, options.numThreads )
154
155 if options.indexRepeatMasker:
156 all_index_cmds += " -R"
157
158 if options.indexContigOptions:
159 index_contig_options = map( int, options.indexContigOptions.split( ',' ) )
160 if index_contig_options[0] >= 0:
161 all_index_cmds += ' -s "%s"' % index_contig_options[0]
162 if index_contig_options[1] >= 0:
163 all_index_cmds += ' -S "%s"' % index_contig_options[1]
164 if index_contig_options[2] >= 0:
165 all_index_cmds += ' -e "%s"' % index_contig_options[2]
166 if index_contig_options[3] >= 0:
167 all_index_cmds += ' -E "%s"' % index_contig_options[3]
168 elif options.indexExonsFileName:
169 all_index_cmds += ' -x "%s"' % options.indexExonsFileName
170
171 index_count = 1
172 for mask, hash_width in [ mask.split( ':' ) for mask in options.indexMask.split( ',' ) ]:
173 cmd = '%s -m "%s" -w "%s" -i "%i"' % ( all_index_cmds, mask, hash_width, index_count )
174 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
175 tmp_stderr = open( tmp, 'wb' )
176 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
177 returncode = proc.wait()
178 tmp_stderr.close()
179 # get stderr, allowing for case where it's very large
180 tmp_stderr = open( tmp, 'rb' )
181 stderr = ''
182 try:
183 while True:
184 stderr += tmp_stderr.read( buffsize )
185 if not stderr or len( stderr ) % buffsize != 0:
186 break
187 except OverflowError:
188 pass
189 tmp_stderr.close()
190 if returncode != 0:
191 raise Exception, stderr
192 index_count += 1
193 except Exception, e:
194 raise Exception, 'Error in \'bfast index\'.\n' + str( e )
195
196 else:
197 reference_filepath = options.ref
198 assert reference_filepath and os.path.exists( reference_filepath ), 'A valid genome reference was not provided.'
199
200 # set up aligning and generate aligning command options
201 # set up temp output files
202 tmp_bmf = tempfile.NamedTemporaryFile( dir=tmp_dir )
203 tmp_bmf_name = tmp_bmf.name
204 tmp_bmf.close()
205 tmp_baf = tempfile.NamedTemporaryFile( dir=tmp_dir )
206 tmp_baf_name = tmp_baf.name
207 tmp_baf.close()
208
209 bfast_match_cmd = 'bfast match -f "%s" -r "%s" -n "%s" -A "%s" -T "%s" -w "%s" %s' % ( reference_filepath, options.fastq, options.numThreads, options.space, tmp_dir, options.whichStrand, all_cmd_options )
210 bfast_localalign_cmd = 'bfast localalign -f "%s" -m "%s" -n "%s" -A "%s" -o "%s" %s' % ( reference_filepath, tmp_bmf_name, options.numThreads, options.space, options.offset, all_cmd_options )
211 bfast_postprocess_cmd = 'bfast postprocess -O 1 -f "%s" -i "%s" -n "%s" -A "%s" -a "%s" %s' % ( reference_filepath, tmp_baf_name, options.numThreads, options.space, options.algorithm, all_cmd_options )
212
213 if options.offsets:
214 bfast_match_cmd += ' -o "%s"' % options.offsets
215 if options.keySize >= 0:
216 bfast_match_cmd += ' -k "%s"' % options.keySize
217 if options.maxKeyMatches >= 0:
218 bfast_match_cmd += ' -K "%s"' % options.maxKeyMatches
219 if options.maxNumMatches >= 0:
220 bfast_match_cmd += ' -M "%s"' % options.maxNumMatches
221 bfast_localalign_cmd += ' -M "%s"' % options.maxNumMatches
222 if options.scoringMatrixFileName:
223 bfast_localalign_cmd += ' -x "%s"' % options.scoringMatrixFileName
224 bfast_postprocess_cmd += ' -x "%s"' % options.scoringMatrixFileName
225 if options.ungapped:
226 bfast_localalign_cmd += ' -u'
227 if options.unconstrained:
228 bfast_localalign_cmd += ' -U'
229 if options.avgMismatchQuality >= 0:
230 bfast_localalign_cmd += ' -q "%s"' % options.avgMismatchQuality
231 bfast_postprocess_cmd += ' -q "%s"' % options.avgMismatchQuality
232 if options.algorithm == 3:
233 if options.pairedEndInfer:
234 bfast_postprocess_cmd += ' -P'
235 if options.randomBest:
236 bfast_postprocess_cmd += ' -z'
237 if options.unpaired:
238 bfast_postprocess_cmd += ' -U'
239 if options.reverseStrand:
240 bfast_postprocess_cmd += ' -R'
241
242 #instead of using temp files, should we stream through pipes?
243 bfast_match_cmd += " > %s" % tmp_bmf_name
244 bfast_localalign_cmd += " > %s" % tmp_baf_name
245 bfast_postprocess_cmd += " > %s" % options.output
246
247 # need to nest try-except in try-finally to handle 2.4
248 try:
249 # bfast 'match'
250 try:
251 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
252 tmp_stderr = open( tmp, 'wb' )
253 proc = subprocess.Popen( args=bfast_match_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
254 returncode = proc.wait()
255 tmp_stderr.close()
256 # get stderr, allowing for case where it's very large
257 tmp_stderr = open( tmp, 'rb' )
258 stderr = ''
259 try:
260 while True:
261 stderr += tmp_stderr.read( buffsize )
262 if not stderr or len( stderr ) % buffsize != 0:
263 break
264 except OverflowError:
265 pass
266 tmp_stderr.close()
267 if returncode != 0:
268 raise Exception, stderr
269 except Exception, e:
270 raise Exception, 'Error in \'bfast match\'. \n' + str( e )
271 # bfast 'localalign'
272 try:
273 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
274 tmp_stderr = open( tmp, 'wb' )
275 proc = subprocess.Popen( args=bfast_localalign_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
276 returncode = proc.wait()
277 tmp_stderr.close()
278 # get stderr, allowing for case where it's very large
279 tmp_stderr = open( tmp, 'rb' )
280 stderr = ''
281 try:
282 while True:
283 stderr += tmp_stderr.read( buffsize )
284 if not stderr or len( stderr ) % buffsize != 0:
285 break
286 except OverflowError:
287 pass
288 tmp_stderr.close()
289 if returncode != 0:
290 raise Exception, stderr
291 except Exception, e:
292 raise Exception, 'Error in \'bfast localalign\'. \n' + str( e )
293 # bfast 'postprocess'
294 try:
295 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
296 tmp_stderr = open( tmp, 'wb' )
297 proc = subprocess.Popen( args=bfast_postprocess_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
298 returncode = proc.wait()
299 tmp_stderr.close()
300 # get stderr, allowing for case where it's very large
301 tmp_stderr = open( tmp, 'rb' )
302 stderr = ''
303 try:
304 while True:
305 stderr += tmp_stderr.read( buffsize )
306 if not stderr or len( stderr ) % buffsize != 0:
307 break
308 except OverflowError:
309 pass
310 tmp_stderr.close()
311 if returncode != 0:
312 raise Exception, stderr
313 except Exception, e:
314 raise Exception, 'Error in \'bfast postprocess\'. \n' + str( e )
315 # remove header if necessary
316 if options.suppressHeader:
317 tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
318 tmp_out_name = tmp_out.name
319 tmp_out.close()
320 try:
321 shutil.move( options.output, tmp_out_name )
322 except Exception, e:
323 raise Exception, 'Error moving output file before removing headers. \n' + str( e )
324 fout = file( options.output, 'w' )
325 for line in file( tmp_out.name, 'r' ):
326 if len( line ) < 3 or line[0:3] not in [ '@HD', '@SQ', '@RG', '@PG', '@CO' ]:
327 fout.write( line )
328 fout.close()
329 # check that there are results in the output file
330 if os.path.getsize( options.output ) > 0:
331 if "0" == options.space:
332 sys.stdout.write( 'BFAST run on Base Space data' )
333 else:
334 sys.stdout.write( 'BFAST run on Color Space data' )
335 else:
336 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.'
337 except Exception, e:
338 stop_err( 'The alignment failed.\n' + str( e ) )
339 finally:
340 # clean up temp dir
341 if os.path.exists( tmp_dir ):
342 shutil.rmtree( tmp_dir )
343
344 if __name__=="__main__": __main__()