comparison SMART/DiffExpAnal/tophat_parallel.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1
2 #!/usr/bin/env python
3
4 import optparse, os, shutil, subprocess, sys, tempfile, fileinput, tarfile,random
5
6 def stop_err( msg ):
7 sys.stderr.write( "%s\n" % msg )
8 sys.exit()
9
10 def toTar(tarFileName, accepted_hits_outputNames):
11 fileName = os.path.splitext(tarFileName)[0]
12 fileNameBaseName = os.path.basename(fileName)
13 dir = os.path.dirname(tarFileName)
14 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
15 currentPath = os.getcwd()
16 os.chdir(dir)
17 for file in accepted_hits_outputNames:
18 relativeFileName = os.path.basename(file)
19 tfile.add(relativeFileName)
20 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
21 tfile.close()
22 os.chdir(currentPath)
23
24
25 def __main__():
26 #Parse Command Line
27 parser = optparse.OptionParser()
28 parser.add_option('-o', '--outputTxtFile', dest='outputTxtFile', help='for Differential expression analysis pipeline, new output option gives a txt output containing the list of mapping results.')
29 parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all accepted hits results in a tar file.' )
30 parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
31 parser.add_option( '-C', '--color-space', dest='color_space', action='store_true', help='This indicates color-space data' )
32 parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', default='junctions_output.bed', help='Junctions output file; formate is BED.' )
33 parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', default='hits_output_%s.bam' % random.randrange(0, 10000), help='Accepted hits output file; formate is BAM.' )
34 parser.add_option( '', '--own-file', dest='own_file', help='' )
35 parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' )
36 parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \
37 For, example, for paired end runs with fragments selected at 300bp, \
38 where each end is 50bp, you should set -r to be 200. There is no default, \
39 and this parameter is required for paired end runs.')
40 parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' )
41 parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length',
42 help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' )
43 parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' )
44 parser.add_option( '-i', '--min-intron-length', dest='min_intron_length',
45 help='The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.' )
46 parser.add_option( '-I', '--max-intron-length', dest='max_intron_length',
47 help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' )
48 parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' )
49 parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
50 parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' )
51 parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
52 parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
53 parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' )
54 parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)' )
55 parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' )
56 parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' )
57
58 # Options for supplying own junctions
59 parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \
60 TopHat will use the exon records in this file to build \
61 a set of known splice junctions for each gene, and will \
62 attempt to align reads to these junctions even if they \
63 would not normally be covered by the initial mapping.')
64 parser.add_option( '-j', '--raw-juncs', dest='raw_juncs', help='Supply TopHat with a list of raw junctions. Junctions are \
65 specified one per line, in a tab-delimited format. Records \
66 look like: <chrom> <left> <right> <+/-> left and right are \
67 zero-based coordinates, and specify the last character of the \
68 left sequenced to be spliced to the first character of the right \
69 sequence, inclusive.')
70 parser.add_option( '', '--no-novel-juncs', action="store_true", dest='no_novel_juncs', help="Only look for junctions indicated in the \
71 supplied GFF file. (ignored without -G)")
72 parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
73 # Types of search.
74 parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.')
75 parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)')
76 parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' )
77 parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.')
78 parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' )
79 parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' )
80 parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' )
81 parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' )
82 parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' )
83 parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
84 parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
85 parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
86
87 # Wrapper options.
88 parser.add_option( '-1', '--input1', dest='input1', help='A list of the (forward or single-end) reads files of Sanger FASTQ format, txt format' )
89 #parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
90 #parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
91 parser.add_option( '-2', '--input2', dest='input2', help='The list of reverse reads file in Sanger FASTQ format' )
92 parser.add_option( '', '--single-paired', dest='single_paired', help='' )
93 parser.add_option( '', '--settings', dest='settings', help='' )
94
95 (options, args) = parser.parse_args()
96
97 # output version # of tool
98 try:
99 tmp_files = []
100 tmp = tempfile.NamedTemporaryFile().name
101 tmp_files.append(tmp)
102 tmp_stdout = open( tmp, 'wb' )
103 proc = subprocess.Popen( args='tophat -v', shell=True, stdout=tmp_stdout )
104 tmp_stdout.close()
105 returncode = proc.wait()
106 stdout = open( tmp_stdout.name, 'rb' ).readline().strip()
107 if stdout:
108 sys.stdout.write( '%s\n' % stdout )
109 else:
110 raise Exception
111 except:
112 sys.stdout.write( 'Could not determine Tophat version\n' )
113
114 # Color or base space
115 space = ''
116 if options.color_space:
117 space = '-C'
118
119
120 #reads = options.input1
121 file = open(options.input1,"r")
122 lines = file.readlines()
123 inputFileNames = []
124 accepted_hits_outputNames = []
125 outputName = options.outputTxtFile
126 resDirName = os.path.dirname(outputName) + '/'
127 out = open(outputName, "w")
128 for line in lines:
129 tab = line.split()
130 inputFileNames.append(tab[1])
131 aHitOutName = resDirName + tab[0] + '_' + options.accepted_hits_output_file
132 accepted_hits_outputNames.append(aHitOutName)
133 out.write(tab[0] + '\t' + aHitOutName + '\n')
134 file.close()
135 out.close()
136
137 if options.input2:
138 revFile = open(options.input2,"r")
139 lines = revFile.readlines()
140 inputRevFileNames = []
141 for line in lines:
142 revTab = line.split()
143 inputRevFileNames.append(revTab[1])
144 revFile.close()
145
146
147 # Creat bowtie index if necessary.
148 tmp_index_dirs = []
149 index_paths = []
150 tmp_index_dir = tempfile.mkdtemp()
151 tmp_index_dirs.append(tmp_index_dir)
152 if options.own_file:
153 index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
154 index_paths.append(index_path)
155 try:
156 os.link( options.own_file, index_path + '.fa' )
157 except:
158 # Tophat prefers (but doesn't require) fasta file to be in same directory, with .fa extension
159 pass
160 cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file, index_path )
161 try:
162 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
163 tmp_stderr = open( tmp, 'wb' )
164 proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
165 returncode = proc.wait()
166 tmp_stderr.close()
167 # get stderr, allowing for case where it's very large
168 tmp_stderr = open( tmp, 'rb' )
169 stderr = ''
170 buffsize = 1048576
171 try:
172 while True:
173 stderr += tmp_stderr.read( buffsize )
174 if not stderr or len( stderr ) % buffsize != 0:
175 break
176 except OverflowError:
177 pass
178 tmp_stderr.close()
179 if returncode != 0:
180 raise Exception, stderr
181 except Exception, e:
182 if os.path.exists( tmp_index_dir ):
183 shutil.rmtree( tmp_index_dir )
184 stop_err( 'Error indexing reference sequence\n' + str( e ) )
185 else:
186 for file in inputFileNames:
187 tmp_index_dir = tempfile.mkdtemp()
188 index_path = tmp_index_dir + '/' + os.path.basename(file).split('.')[0]
189 index_paths.append(index_path)
190 tmp_index_dirs.append(tmp_index_dir)
191
192
193
194 # Build tophat command.
195 cmds = []
196 # for inputFileName in inputFileNames:
197 for i in range(len(inputFileNames)):
198 cmd = 'tophat %s %s %s '
199 input_files = inputFileNames[i]
200 if options.input2:
201 input_files += ' ' + inputRevFileNames[i]
202 opts = '-p %s %s' % ( options.num_threads, space )
203 if options.single_paired == 'paired':
204 opts += '-r %s ' % options.mate_inner_dist
205 if options.settings == 'preSet':
206 if options.own_file:
207 cmd = cmd % ( opts, index_paths[0], input_files ) #here add paired end file
208 else:
209 cmd = cmd % ( opts, index_paths[i], input_files ) #here add paired end file
210 else:
211 try:
212 if int( options.min_anchor_length ) >= 3:
213 opts += '-a %s ' % options.min_anchor_length
214 else:
215 raise Exception, 'Minimum anchor length must be 3 or greater'
216 opts += '-m %s ' % options.splice_mismatches
217 opts += '-i %s ' % options.min_intron_length
218 opts += '-I %s ' % options.max_intron_length
219 if float( options.junction_filter ) != 0.0:
220 opts += '-F %s ' % options.junction_filter
221 opts += '-g %s ' % options.max_multihits
222 # Custom junctions options.
223 if options.gene_model_annotations:
224 opts += '-G %s ' % options.gene_model_annotations
225 if options.raw_juncs:
226 opts += '-j %s ' % options.raw_juncs
227 if options.no_novel_juncs:
228 opts += '--no-novel-juncs '
229 if options.library_type:
230 opts += '--library-type %s ' % options.library_type
231 if options.no_novel_indels:
232 opts += '--no-novel-indels '
233 else:
234 if options.max_insertion_length:
235 opts += '--max-insertion-length %i ' % int( options.max_insertion_length )
236 if options.max_deletion_length:
237 opts += '--max-deletion-length %i ' % int( options.max_deletion_length )
238 # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
239 # need to warn user of this fact
240 #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
241
242 # Search type options.
243 if options.coverage_search:
244 opts += '--coverage-search --min-coverage-intron %s --max-coverage-intron %s ' % ( options.min_coverage_intron, options.max_coverage_intron )
245 else:
246 opts += '--no-coverage-search '
247 if options.closure_search:
248 opts += '--closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s ' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron )
249 else:
250 opts += '--no-closure-search '
251 if options.microexon_search:
252 opts += '--microexon-search '
253 if options.single_paired == 'paired':
254 opts += '--mate-std-dev %s ' % options.mate_std_dev
255 if options.initial_read_mismatches:
256 opts += '--initial-read-mismatches %d ' % int( options.initial_read_mismatches )
257 if options.seg_mismatches:
258 opts += '--segment-mismatches %d ' % int( options.seg_mismatches )
259 if options.seg_length:
260 opts += '--segment-length %d ' % int( options.seg_length )
261 if options.min_segment_intron:
262 opts += '--min-segment-intron %d ' % int( options.min_segment_intron )
263 if options.max_segment_intron:
264 opts += '--max-segment-intron %d ' % int( options.max_segment_intron )
265 if options.own_file:
266 cmd = cmd % ( opts, index_paths[0], input_files ) #here to add paired end file
267 else:
268 cmd = cmd % ( opts, index_paths[i], input_files ) #here to add paired end file
269 except Exception, e:
270 # Clean up temp dirs
271 if os.path.exists( tmp_index_dir ):
272 shutil.rmtree( tmp_index_dir )
273 stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
274
275 cmds.append(cmd)
276
277 # Run the command line for each file.
278 for i in range(len(cmds)):
279 try:
280 tmp_out = tempfile.NamedTemporaryFile().name
281 tmp_files.append(tmp_out)
282 tmp_stdout = open( tmp_out, 'wb' )
283 tmp_err = tempfile.NamedTemporaryFile().name
284 tmp_files.append(tmp_err)
285 tmp_stderr = open( tmp_err, 'wb' )
286 proc = subprocess.Popen( args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
287 returncode = proc.wait()
288 tmp_stderr.close()
289 # get stderr, allowing for case where it's very large
290 tmp_stderr = open( tmp_err, 'rb' )
291 stderr = ''
292 buffsize = 1048576
293 try:
294 while True:
295 stderr += tmp_stderr.read( buffsize )
296 if not stderr or len( stderr ) % buffsize != 0:
297 break
298 except OverflowError:
299 pass
300 tmp_stdout.close()
301 tmp_stderr.close()
302 if returncode != 0:
303 raise Exception, stderr
304
305 # Copy output files from tmp directory to specified files.
306 #shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), junctions_outputNames[i] )
307 shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), accepted_hits_outputNames[i] )
308 # TODO: look for errors in program output.
309 except Exception, e:
310 stop_err( 'Error in tophat:\n' + str( e ) )
311
312 if options.outputTar != None:
313 toTar(options.outputTar, accepted_hits_outputNames)
314
315
316 # Clean up temp dirs
317 for tmp_index_dir in tmp_index_dirs:
318 if os.path.exists( tmp_index_dir ):
319 shutil.rmtree( tmp_index_dir )
320
321 for tmp in tmp_files:
322 os.remove(tmp)
323
324
325 if __name__=="__main__": __main__()