root/galaxy-central/tools/sr_mapping/bowtie_wrapper.py

リビジョン 2, 23.5 KB (コミッタ: hatakeyama, 15 年 前)

import galaxy-central
行番号 
1#!/usr/bin/env python
2
3"""
4Runs Bowtie on single-end or paired-end data.
5For use with Bowtie v. 0.12.3
6
7usage: bowtie_wrapper.py [options]
8    -t, --threads=t: The number of threads to run
9    -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
10    -I, --input2=I: The reverse reads file in Sanger FASTQ format
11    -o, --output=o: The output file
12    -4, --dataType=4: The type of data (SOLiD or Solexa)
13    -2, --paired=2: Whether the data is single- or paired-end
14    -g, --genomeSource=g: The type of reference provided
15    -r, --ref=r: The reference genome to use or index
16    -s, --skip=s: Skip the first n reads
17    -a, --alignLimit=a: Only align the first n reads
18    -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
19    -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
20    -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
21    -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
22    -l, --seedLen=l: Seed length
23    -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
24    -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy
25    -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
26    -v, --valAlign=v: Report up to n valid arguments per read
27    -V, --allValAligns=V: Whether or not to report all valid alignments per read
28    -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
29    -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions
30    -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
31    -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
32    -j, --minInsert=j: Minimum insert size for valid paired-end alignments
33    -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
34    -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
35    -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
36    -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
37    -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
38    -F, --offrate=F: Override the offrate of the index to n
39    -8, --snpphred=8: SNP penalty on Phred scale
40    -6, --snpfrac=6: Fraction of sites expected to be SNP sites
41    -7, --keepends=7: Keep extreme-end nucleotides and qualities
42    -S, --seed=S: Seed for pseudo-random number generator
43    -C, --params=C: Whether to use default or specified parameters
44    -u, --iautoB=u: Automatic or specified behavior
45    -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
46    -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
47    -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
48    -D, --idcv=D: The period for the difference-cover sample
49    -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
50    -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
51    -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
52    -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
53    -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
54    -N, --iendian=N: Endianness to use when serializing integers to the index file
55    -Z, --iseed=Z: Seed for the pseudorandom number generator
56    -c, --icutoff=c: Number of first bases of the reference sequence to index
57    -x, --indexSettings=x: Whether or not indexing options are to be set
58    -H, --suppressHeader=H: Suppress header
59    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
60"""
61
62import optparse, os, shutil, subprocess, sys, tempfile
63
64def stop_err( msg ):
65    sys.stderr.write( '%s\n' % msg )
66    sys.exit()
67
68def __main__():
69    #Parse Command Line
70    parser = optparse.OptionParser()
71    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
72    parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
73    parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
74    parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
75    parser.add_option( '-o', '--output', dest='output', help='The output file' )
76    parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
77    parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
78    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
79    parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
80    parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
81    parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
82    parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
83    parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
84    parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
85    parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
86    parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
87    parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' )
88    parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
89    parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' )
90    parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' )
91    parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
92    parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" )
93    parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
94    parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
95    parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
96    parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
97    parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
98    parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
99    parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
100    parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
101    parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
102    parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
103    parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
104    parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
105    parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
106    parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
107    parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
108    parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
109    parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
110    parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
111    parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
112    parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
113    parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
114    parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
115    parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
116    parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
117    parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
118    parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
119    parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' )
120    parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
121    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
122    parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
123    (options, args) = parser.parse_args()
124    stdout = ''
125
126    # make temp directory for placement of indices and copy reference file there if necessary
127    tmp_index_dir = tempfile.mkdtemp()
128    # get type of data (solid or solexa)
129    if options.dataType == 'solid':
130        colorspace = '-C'
131    else:
132        colorspace = ''
133    # index if necessary
134    if options.genomeSource == 'history' and not options.do_not_build_index:
135        # set up commands
136        if options.index_settings =='indexPreSet':
137            indexing_cmds = '%s' % colorspace
138        else:
139            try:
140                if options.iautoB != 'None' and options.iautoB == 'set':
141                    iautoB = '--noauto'
142                else:
143                    iautoB = ''
144                if options. ipacked != 'None' and options.ipacked == 'packed':
145                    ipacked = '--packed'
146                else:
147                    ipacked = ''
148                if options.ibmax != 'None' and int( options.ibmax ) >= 1:
149                    ibmax = '--bmax %s' % options.ibmax
150                else:
151                    ibmax = ''
152                if options.ibmaxdivn != 'None' and int( options.ibmaxdivn ) >= 0:
153                    ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
154                else:
155                    ibmaxdivn = ''
156                if options.idcv != 'None' and int( options.idcv ) > 0:
157                    idcv = '--dcv %s' % options.idcv
158                else:
159                    idcv = ''
160                if options.inodc != 'None' and options.inodc == 'nodc':
161                    inodc = '--nodc'
162                else:
163                    inodc = ''
164                if options.inoref != 'None' and options.inoref == 'noref':
165                    inoref = '--noref'
166                else:
167                    inoref = ''
168                if options.iftab != 'None' and int( options.iftab ) >= 0:
169                    iftab = '--ftabchars %s' % options.iftab
170                else:
171                    iftab = ''
172                if options.intoa != 'None' and options.intoa == 'yes':
173                    intoa = '--ntoa'
174                else:
175                    intoa = ''
176                if options.iendian != 'None' and options.iendian == 'big':
177                    iendian = '--big'
178                else:
179                    iendian = '--little'
180                if options.iseed != 'None' and int( options.iseed ) > 0:
181                    iseed = '--seed %s' % options.iseed
182                else:
183                    iseed = ''
184                if options.icutoff != 'None' and int( options.icutoff ) > 0:
185                    icutoff = '--cutoff %s' % options.icutoff
186                else:
187                    icutoff = ''
188                indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
189                                ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
190                                  inoref, options.ioffrate, iftab, intoa, iendian,
191                                  iseed, icutoff, colorspace )
192            except ValueError, e:
193                # clean up temp dir
194                if os.path.exists( tmp_index_dir ):
195                    shutil.rmtree( tmp_index_dir )
196                stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
197        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
198        ref_file_name = ref_file.name
199        ref_file.close()
200        os.symlink( options.ref, ref_file_name )
201        cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
202        try:
203            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
204            tmp_stderr = open( tmp, 'wb' )
205            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
206            returncode = proc.wait()
207            tmp_stderr.close()
208            # get stderr, allowing for case where it's very large
209            tmp_stderr = open( tmp, 'rb' )
210            stderr = ''
211            buffsize = 1048576
212            try:
213                while True:
214                    stderr += tmp_stderr.read( buffsize )
215                    if not stderr or len( stderr ) % buffsize != 0:
216                        break
217            except OverflowError:
218                pass
219            tmp_stderr.close()
220            if returncode != 0:
221                raise Exception, stderr
222        except Exception, e:
223            # clean up temp dir
224            if os.path.exists( tmp_index_dir ):
225                shutil.rmtree( tmp_index_dir )
226            stop_err( 'Error indexing reference sequence\n' + str( e ) )
227        stdout += 'File indexed. '
228    else:
229        ref_file_name = options.ref
230    # set up aligning and generate aligning command options
231    # automatically set threads in both cases
232    if options.suppressHeader == 'true':
233        suppressHeader = '--sam-nohead'
234    else:
235        suppressHeader = ''
236    if options.maxInsert != 'None' and int( options.maxInsert ) > 0:
237        maxInsert = '-X %s' % options.maxInsert
238    else:
239        maxInsert = ''
240    if options.mateOrient != 'None':
241        mateOrient = '--%s' % options.mateOrient
242    else:
243        mateOrient = ''
244    if options.params == 'preSet':
245        aligning_cmds = '%s %s -p %s -S %s -q %s ' % \
246                ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace )
247    else:
248        try:
249            if options.skip != 'None' and int( options.skip ) > 0:
250                skip = '-s %s' % options.skip
251            else:
252                skip = ''
253            if options.alignLimit != 'None' and int( options.alignLimit ) >= 0:
254                alignLimit = '-u %s' % options.alignLimit
255            else:
256                alignLimit = ''
257            if options.trimH != 'None' and int( options.trimH ) > 0:
258                trimH = '-5 %s' % options.trimH
259            else:
260                trimH = ''
261            if options.trimL != 'None' and int( options.trimL ) > 0:
262                trimL = '-3 %s' % options.trimL
263            else:
264                trimL = ''
265            if options.mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
266                        or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
267                mismatchSeed = '-n %s' % options.mismatchSeed
268            else:
269                mismatchSeed = ''
270            if options.mismatchQual != 'None' and int( options.mismatchQual ) >= 0:
271                mismatchQual = '-e %s' % options.mismatchQual
272            else:
273                mismatchQual = ''
274            if options.seedLen != 'None' and int( options.seedLen ) >= 5:
275                seedLen = '-l %s' % options.seedLen
276            else:
277                seedLen = ''
278            if options.rounding == 'noRound':
279                rounding = '--nomaqround'
280            else:
281                rounding = ''
282            if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0:
283                maqSoapAlign = '-v %s' % options.maqSoapAlign
284            else:
285                maqSoapAlign = ''
286            if options.minInsert != 'None' and int( options.minInsert ) > 0:
287                minInsert = '-I %s' % options.minInsert
288            else:
289                minInsert = ''
290            if options.maxAlignAttempt != 'None' and int( options.maxAlignAttempt ) >= 0:
291                maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
292            else:
293                maxAlignAttempt = ''
294            if options.forwardAlign == 'noForward':
295                forwardAlign = '--nofw'
296            else:
297                forwardAlign = ''
298            if options.reverseAlign == 'noReverse':
299                reverseAlign = '--norc'
300            else:
301                reverseAlign = ''
302            if options.maxBacktracks != 'None' and int( options.maxBacktracks ) > 0 and \
303                    ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
304                maxBacktracks = '--maxbts %s' % options.maxBacktracks
305            else:
306                maxBacktracks = ''
307            if options.tryHard == 'doTryHard':
308                tryHard = '-y'
309            else:
310                tryHard = ''
311            if options.valAlign != 'None' and int( options.valAlign ) >= 0:
312                valAlign = '-k %s' % options.valAlign
313            else:
314                valAlign = ''
315            if options.allValAligns == 'doAllValAligns':
316                allValAligns = '-a'
317            else:
318                allValAligns = ''
319            if options.suppressAlign != 'None' and int( options.suppressAlign ) >= 0:
320                suppressAlign = '-m %s' % options.suppressAlign
321            else:
322                suppressAlign = ''
323            if options.best == 'doBest':
324                best = '--best'
325            else:
326                best = ''
327            if options.strata == 'doStrata':
328                strata = '--strata'
329            else:
330                strata = ''
331            if options.offrate != 'None' and int( options.offrate ) >= 0:
332                offrate = '-o %s' % options.offrate
333            else:
334                offrate = ''
335            if options.seed != 'None' and int( options.seed ) >= 0:
336                seed = '--seed %s' % options.seed
337            else:
338                seed = ''
339            if options.snpphred != 'None' and int( options.snpphred ) >= 0:
340                snpphred = '--snpphred %s' % options.snpphred
341            else:
342                snpphred = ''
343                if options.snpfrac != 'None' and float( options.snpfrac ) >= 0:
344                    snpfrac = '--snpfrac %s' % options.snpfrac
345                else:
346                    snpfrac = ''
347            if options.keepends != 'None' and options.keepends == 'doKeepends':
348                keepends = '--col-keepends'
349            else:
350                keepends = ''
351            aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \
352                            '%s %s %s %s %s %s %s %s %s %s %s -p %s -S %s -q' % \
353                            ( skip, alignLimit, trimH, trimL, mismatchSeed, mismatchQual,
354                              seedLen, rounding, maqSoapAlign, minInsert, maxInsert,
355                              mateOrient, maxAlignAttempt, forwardAlign, reverseAlign,
356                              maxBacktracks, tryHard, valAlign, allValAligns, suppressAlign,
357                              best, strata, offrate, seed, colorspace, snpphred, snpfrac,
358                              keepends, options.threads, suppressHeader )
359        except ValueError, e:
360            # clean up temp dir
361            if os.path.exists( tmp_index_dir ):
362                shutil.rmtree( tmp_index_dir )
363            stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
364    try:
365        # have to nest try-except in try-finally to handle 2.4
366        try:
367            # prepare actual aligning commands
368            if options.paired == 'paired':
369                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
370            else:
371                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
372            # align
373            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
374            tmp_stderr = open( tmp, 'wb' )
375            proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
376            returncode = proc.wait()
377            tmp_stderr.close()
378            # get stderr, allowing for case where it's very large
379            tmp_stderr = open( tmp, 'rb' )
380            stderr = ''
381            buffsize = 1048576
382            try:
383                while True:
384                    stderr += tmp_stderr.read( buffsize )
385                    if not stderr or len( stderr ) % buffsize != 0:
386                        break
387            except OverflowError:
388                pass
389            tmp_stderr.close()
390            if returncode != 0:
391                raise Exception, stderr
392            # check that there are results in the output file
393            if os.path.getsize( options.output ) == 0:
394                raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + '\nextra: ' + str(extra)
395        except Exception, e:
396            stop_err( 'Error aligning sequence. ' + str( e ) )
397    finally:
398        # clean up temp dir
399        if os.path.exists( tmp_index_dir ):
400            shutil.rmtree( tmp_index_dir )
401    stdout += 'Sequence file aligned.\n'
402    sys.stdout.write( stdout )
403
404if __name__=="__main__": __main__()
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