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comparison tools/picard/picard_wrapper.py @ 0:9071e359b9a3

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date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env python
2 """
3 Originally written by Kelly Vincent
4 pretty output and additional picard wrappers by Ross Lazarus for rgenetics
5 Runs all available wrapped Picard tools.
6 usage: picard_wrapper.py [options]
7 code Ross wrote licensed under the LGPL
8 see http://www.gnu.org/copyleft/lesser.html
9 """
10
11 import optparse, os, sys, subprocess, tempfile, shutil, time, logging
12
13 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
14 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
15 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
16 <head>
17 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
18 <meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />
19 <title></title>
20 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
21 </head>
22 <body>
23 <div class="document">
24 """
25 galhtmlattr = """Galaxy tool %s run at %s</b><br/>"""
26 galhtmlpostfix = """</div></body></html>\n"""
27
28
29 def stop_err( msg ):
30 sys.stderr.write( '%s\n' % msg )
31 sys.exit()
32
33
34 def timenow():
35 """return current time as a string
36 """
37 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
38
39
40 class PicardBase():
41 """
42 simple base class with some utilities for Picard
43 adapted and merged with Kelly Vincent's code april 2011 Ross
44 lots of changes...
45 """
46
47 def __init__(self, opts=None,arg0=None):
48 """ common stuff needed at init for a picard tool
49 """
50 assert opts <> None, 'PicardBase needs opts at init'
51 self.opts = opts
52 if self.opts.outdir == None:
53 self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir
54 assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in'
55 self.picname = self.baseName(opts.jar)
56 if self.picname.startswith('picard'):
57 self.picname = opts.picard_cmd # special case for some tools like replaceheader?
58 self.progname = self.baseName(arg0)
59 self.version = '0.002'
60 self.delme = [] # list of files to destroy
61 self.title = opts.title
62 self.inputfile = opts.input
63 try:
64 os.makedirs(opts.outdir)
65 except:
66 pass
67 try:
68 os.makedirs(opts.tmpdir)
69 except:
70 pass
71 self.log_filename = os.path.join(self.opts.outdir,'%s.log' % self.picname)
72 self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
73 self.setLogging(logfname=self.log_filename)
74
75 def baseName(self,name=None):
76 return os.path.splitext(os.path.basename(name))[0]
77
78 def setLogging(self,logfname="picard_wrapper.log"):
79 """setup a logger
80 """
81 logging.basicConfig(level=logging.INFO,
82 filename=logfname,
83 filemode='a')
84
85
86 def readLarge(self,fname=None):
87 """ read a potentially huge file.
88 """
89 try:
90 # get stderr, allowing for case where it's very large
91 tmp = open( fname, 'rb' )
92 s = ''
93 buffsize = 1048576
94 try:
95 while True:
96 more = tmp.read( buffsize )
97 if len(more) > 0:
98 s += more
99 else:
100 break
101 except OverflowError:
102 pass
103 tmp.close()
104 except Exception, e:
105 stop_err( 'Error : %s' % str( e ) )
106 return s
107
108 def runCL(self,cl=None,output_dir=None):
109 """ construct and run a command line
110 we have galaxy's temp path as opt.temp_dir so don't really need isolation
111 sometimes stdout is needed as the output - ugly hacks to deal with potentially vast artifacts
112 """
113 assert cl <> None, 'PicardBase runCL needs a command line as cl'
114 if output_dir == None:
115 output_dir = self.opts.outdir
116 if type(cl) == type([]):
117 cl = ' '.join(cl)
118 fd,templog = tempfile.mkstemp(dir=output_dir,suffix='rgtempRun.txt')
119 tlf = open(templog,'wb')
120 fd,temperr = tempfile.mkstemp(dir=output_dir,suffix='rgtempErr.txt')
121 tef = open(temperr,'wb')
122 process = subprocess.Popen(cl, shell=True, stderr=tef, stdout=tlf, cwd=output_dir)
123 rval = process.wait()
124 tlf.close()
125 tef.close()
126 stderrs = self.readLarge(temperr)
127 stdouts = self.readLarge(templog)
128 if len(stderrs) > 0:
129 s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs)
130 else:
131 s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval)
132 logging.info(s)
133 os.unlink(templog) # always
134 os.unlink(temperr) # always
135 return s, stdouts # sometimes this is an output
136
137 def runPic(self, jar, cl):
138 """
139 cl should be everything after the jar file name in the command
140 """
141 runme = ['java -Xmx%s' % self.opts.maxjheap]
142 runme.append('-jar %s' % jar)
143 runme += cl
144 s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir)
145 return stdout
146
147 def samToBam(self,infile=None,outdir=None):
148 """
149 use samtools view to convert sam to bam
150 """
151 fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
152 cl = ['samtools view -h -b -S -o ',tempbam,infile]
153 tlog,stdouts = self.runCL(cl,outdir)
154 return tlog,tempbam
155
156 #def bamToSam(self,infile=None,outdir=None):
157 # """
158 # use samtools view to convert bam to sam
159 # """
160 # fd,tempsam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.sam')
161 # cl = ['samtools view -h -o ',tempsam,infile]
162 # tlog,stdouts = self.runCL(cl,outdir)
163 # return tlog,tempsam
164
165 def sortSam(self, infile=None,outfile=None,outdir=None):
166 """
167 """
168 print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
169 cl = ['samtools sort',infile,outfile]
170 tlog,stdouts = self.runCL(cl,outdir)
171 return tlog
172
173 def cleanup(self):
174 for fname in self.delme:
175 try:
176 os.unlink(fname)
177 except:
178 pass
179
180 def prettyPicout(self,transpose,maxrows):
181 """organize picard outpouts into a report html page
182 """
183 res = []
184 try:
185 r = open(self.metricsOut,'r').readlines()
186 except:
187 r = []
188 if len(r) > 0:
189 res.append('<b>Picard on line resources</b><ul>\n')
190 res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
191 res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n')
192 if transpose:
193 res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n')
194 else:
195 res.append('<b>Picard output</b><hr/>\n')
196 res.append('<table cellpadding="3" >\n')
197 dat = []
198 heads = []
199 lastr = len(r) - 1
200 # special case for estimate library complexity hist
201 thist = False
202 for i,row in enumerate(r):
203 if row.strip() > '':
204 srow = row.split('\t')
205 if row.startswith('#'):
206 heads.append(row.strip()) # want strings
207 else:
208 dat.append(srow) # want lists
209 if row.startswith('## HISTOGRAM'):
210 thist = True
211 if len(heads) > 0:
212 hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)]
213 res += hres
214 heads = []
215 if len(dat) > 0:
216 if transpose and not thist:
217 tdat = map(None,*dat) # transpose an arbitrary list of lists
218 tdat = ['<tr class="d%d"><td>%s</td><td>%s&nbsp;</td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)]
219 else:
220 tdat = ['\t'.join(x).strip() for x in dat] # back to strings :(
221 tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)]
222 res += tdat
223 dat = []
224 res.append('</table>\n')
225 return res
226
227 def fixPicardOutputs(self,transpose,maxloglines):
228 """
229 picard produces long hard to read tab header files
230 make them available but present them transposed for readability
231 """
232 logging.shutdown()
233 self.cleanup() # remove temp files stored in delme
234 rstyle="""<style type="text/css">
235 tr.d0 td {background-color: oldlace; color: black;}
236 tr.d1 td {background-color: aliceblue; color: black;}
237 </style>"""
238 res = [rstyle,]
239 res.append(galhtmlprefix % self.progname)
240 res.append(galhtmlattr % (self.picname,timenow()))
241 flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')]
242 pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
243 if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
244 for p in pdflist:
245 imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf
246 res.append('<table cellpadding="10"><tr><td>\n')
247 res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref))
248 res.append('</tr></td></table>\n')
249 if len(flist) > 0:
250 res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>')
251 res.append('<table>\n')
252 for i,f in enumerate(flist):
253 fn = os.path.split(f)[-1]
254 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
255 res.append('</table><p/>\n')
256 pres = self.prettyPicout(transpose,maxloglines)
257 if len(pres) > 0:
258 res += pres
259 l = open(self.log_filename,'r').readlines()
260 llen = len(l)
261 if llen > 0:
262 res.append('<b>Picard Tool Run Log</b><hr/>\n')
263 rlog = ['<pre>',]
264 if llen > maxloglines:
265 n = min(50,int(maxloglines/2))
266 rlog += l[:n]
267 rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines))
268 rlog += l[-n:]
269 else:
270 rlog += l
271 rlog.append('</pre>')
272 if llen > maxloglines:
273 rlog.append('\n<b>## WARNING - %d log lines truncated - <a href="%s">%s</a> contains entire output</b>' % (llen - maxloglines,self.log_filename,self.log_filename))
274 res += rlog
275 else:
276 res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename)
277 res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
278 res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool')
279 res.append(galhtmlpostfix)
280 outf = open(self.opts.htmlout,'w')
281 outf.write(''.join(res))
282 outf.write('\n')
283 outf.close()
284
285 def makePicInterval(self,inbed=None,outf=None):
286 """
287 picard wants bait and target files to have the same header length as the incoming bam/sam
288 a meaningful (ie accurate) representation will fail because of this - so this hack
289 it would be far better to be able to supply the original bed untouched
290 """
291 assert inbed <> None
292 bed = open(inbed,'r').readlines()
293 thead = os.path.join(self.opts.outdir,'tempSamHead.txt')
294 if self.opts.datatype == 'sam':
295 cl = ['samtools view -H -S',self.opts.input,'>',thead]
296 else:
297 cl = ['samtools view -H',self.opts.input,'>',thead]
298 self.runCL(cl=cl,output_dir=self.opts.outdir)
299 head = open(thead,'r').readlines()
300 s = '## got %d rows of header\n' % (len(head))
301 logging.info(s)
302 o = open(outf,'w')
303 o.write(''.join(head))
304 o.write(''.join(bed))
305 o.close()
306 return outf
307
308 def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None):
309 """
310 interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs!
311 Do the work of removing all the error sequences
312 pysam is cool
313 infile = pysam.Samfile( "-", "r" )
314 outfile = pysam.Samfile( "-", "w", template = infile )
315 for s in infile: outfile.write(s)
316
317 errors from ValidateSameFile.jar look like
318 WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing
319 ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary.
320 ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041
321
322 """
323 assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam
324 assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path'
325 removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2]
326 remDict = dict(zip(removeNames,range(len(removeNames))))
327 infile = pysam.Samfile(insam,'rb')
328 info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict))
329 if len(removeNames) > 0:
330 outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file
331 i = 0
332 j = 0
333 for row in infile:
334 dropme = remDict.get(row.qname,None) # keep if None
335 if not dropme:
336 outfile.write(row)
337 j += 1
338 else: # discard
339 i += 1
340 info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam))
341 outfile.close()
342 infile.close()
343 else: # we really want a nullop or a simple pointer copy
344 infile.close()
345 if newsam:
346 shutil.copy(insam,newsam)
347 logging.info(info)
348
349
350
351 def __main__():
352 doFix = False # tools returning htmlfile don't need this
353 doTranspose = True # default
354 maxloglines = 100 # default
355 #Parse Command Line
356 op = optparse.OptionParser()
357 # All tools
358 op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' )
359 op.add_option('-e', '--inputext', default=None)
360 op.add_option('-o', '--output', default=None)
361 op.add_option('-n', '--title', default="Pick a Picard Tool")
362 op.add_option('-t', '--htmlout', default=None)
363 op.add_option('-d', '--outdir', default=None)
364 op.add_option('-x', '--maxjheap', default='4g')
365 op.add_option('-b', '--bisulphite', default='false')
366 op.add_option('-s', '--sortorder', default='query')
367 op.add_option('','--tmpdir', default='/tmp')
368 op.add_option('-j','--jar',default='')
369 op.add_option('','--picard-cmd',default=None)
370 # Many tools
371 op.add_option( '', '--output-format', dest='output_format', help='Output format' )
372 op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' )
373 op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None )
374 # CreateSequenceDictionary
375 op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None )
376 op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' )
377 op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' )
378 op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' )
379 # MarkDuplicates
380 op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' )
381 op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' )
382 # CollectInsertSizeMetrics
383 op.add_option('', '--taillimit', default="0")
384 op.add_option('', '--histwidth', default="0")
385 op.add_option('', '--minpct', default="0.01")
386 # CollectAlignmentSummaryMetrics
387 op.add_option('', '--maxinsert', default="20")
388 op.add_option('', '--adaptors', action='append', type="string")
389 # FixMateInformation and validate
390 # CollectGcBiasMetrics
391 op.add_option('', '--windowsize', default='100')
392 op.add_option('', '--mingenomefrac', default='0.00001')
393 # AddOrReplaceReadGroups
394 op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' )
395 op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' )
396 op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' )
397 op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' )
398 op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' )
399 op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' )
400 op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' )
401 op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' )
402 # ReorderSam
403 op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' )
404 op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' )
405 # ReplaceSamHeader
406 op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' )
407
408 op.add_option('','--assumesorted', default='true')
409 op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*")
410 #estimatelibrarycomplexity
411 op.add_option('','--minid', default="5")
412 op.add_option('','--maxdiff', default="0.03")
413 op.add_option('','--minmeanq', default="20")
414 #hsmetrics
415 op.add_option('','--baitbed', default=None)
416 op.add_option('','--targetbed', default=None)
417 #validate
418 op.add_option('','--ignoreflags', action='append', type="string")
419 op.add_option('','--maxerrors', default=None)
420 op.add_option('','--datatype', default=None)
421 op.add_option('','--bamout', default=None)
422 op.add_option('','--samout', default=None)
423
424 opts, args = op.parse_args()
425 opts.sortme = opts.assumesorted == 'false'
426 assert opts.input <> None
427 # need to add
428 # instance that does all the work
429 pic = PicardBase(opts,sys.argv[0])
430
431 tmp_dir = opts.outdir
432 haveTempout = False # we use this where sam output is an option
433
434 # set ref and dict files to use (create if necessary)
435 ref_file_name = opts.ref
436 if opts.ref_file <> None:
437 csd = 'CreateSequenceDictionary'
438 realjarpath = os.path.split(opts.jar)[0]
439 jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
440 tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
441 ref_file_name = '%s.fasta' % tmp_ref_name
442 # build dict
443 dict_file_name = '%s.dict' % tmp_ref_name
444 os.symlink( opts.ref_file, ref_file_name )
445 cl = ['REFERENCE=%s' % ref_file_name]
446 cl.append('OUTPUT=%s' % dict_file_name)
447 cl.append('URI=%s' % os.path.basename( opts.ref_file ))
448 cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
449 if opts.species_name:
450 cl.append('SPECIES=%s' % opts.species_name)
451 if opts.build_name:
452 cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
453 pic.delme.append(dict_file_name)
454 pic.delme.append(ref_file_name)
455 pic.delme.append(tmp_ref_name)
456 s = pic.runPic(jarpath, cl)
457 # run relevant command(s)
458
459 # define temporary output
460 # if output is sam, it must have that extension, otherwise bam will be produced
461 # specify sam or bam file with extension
462 if opts.output_format == 'sam':
463 suff = '.sam'
464 else:
465 suff = ''
466 tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff )
467
468 cl = ['VALIDATION_STRINGENCY=LENIENT',]
469
470 if pic.picname == 'AddOrReplaceReadGroups':
471 # sort order to match Galaxy's default
472 cl.append('SORT_ORDER=coordinate')
473 # input
474 cl.append('INPUT=%s' % opts.input)
475 # outputs
476 cl.append('OUTPUT=%s' % tempout)
477 # required read groups
478 cl.append('RGLB="%s"' % opts.rg_library)
479 cl.append('RGPL="%s"' % opts.rg_platform)
480 cl.append('RGPU="%s"' % opts.rg_plat_unit)
481 cl.append('RGSM="%s"' % opts.rg_sample)
482 if opts.rg_id:
483 cl.append('RGID="%s"' % opts.rg_id)
484 # optional read groups
485 if opts.rg_seq_center:
486 cl.append('RGCN="%s"' % opts.rg_seq_center)
487 if opts.rg_desc:
488 cl.append('RGDS="%s"' % opts.rg_desc)
489 pic.runPic(opts.jar, cl)
490 haveTempout = True
491
492 elif pic.picname == 'BamIndexStats':
493 tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir )
494 tmp_bam_name = '%s.bam' % tmp_name
495 tmp_bai_name = '%s.bai' % tmp_bam_name
496 os.symlink( opts.input, tmp_bam_name )
497 os.symlink( opts.bai_file, tmp_bai_name )
498 cl.append('INPUT=%s' % ( tmp_bam_name ))
499 pic.delme.append(tmp_bam_name)
500 pic.delme.append(tmp_bai_name)
501 pic.delme.append(tmp_name)
502 s = pic.runPic( opts.jar, cl )
503 f = open(pic.metricsOut,'a')
504 f.write(s) # got this on stdout from runCl
505 f.write('\n')
506 f.close()
507 doTranspose = False # but not transposed
508
509 elif pic.picname == 'EstimateLibraryComplexity':
510 cl.append('I=%s' % opts.input)
511 cl.append('O=%s' % pic.metricsOut)
512 if float(opts.minid) > 0:
513 cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid)
514 if float(opts.maxdiff) > 0.0:
515 cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff)
516 if float(opts.minmeanq) > 0:
517 cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq)
518 if opts.readregex > '':
519 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
520 if float(opts.optdupdist) > 0:
521 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
522 pic.runPic(opts.jar,cl)
523
524 elif pic.picname == 'CollectAlignmentSummaryMetrics':
525 # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
526 # why? Dunno Seems to work without complaining if the .bai file is AWOL....
527 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
528 try:
529 os.symlink(ref_file_name,fakefasta)
530 except:
531 s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
532 info = s
533 shutil.copy(ref_file_name,fakefasta)
534 pic.delme.append(fakefasta)
535 cl.append('ASSUME_SORTED=%s' % opts.assumesorted)
536 adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors])
537 cl.append(adaptorseqs)
538 cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
539 cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert)
540 cl.append('OUTPUT=%s' % pic.metricsOut)
541 cl.append('R=%s' % fakefasta)
542 cl.append('TMP_DIR=%s' % opts.tmpdir)
543 if not opts.assumesorted.lower() == 'true': # we need to sort input
544 fakeinput = '%s.sorted' % opts.input
545 s = pic.sortSam(opts.input, fakeinput, opts.outdir)
546 pic.delme.append(fakeinput)
547 cl.append('INPUT=%s' % fakeinput)
548 else:
549 cl.append('INPUT=%s' % os.path.abspath(opts.input))
550 pic.runPic(opts.jar,cl)
551
552
553 elif pic.picname == 'CollectGcBiasMetrics':
554 assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name
555 # sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
556 # why? Dunno
557 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
558 try:
559 os.symlink(ref_file_name,fakefasta)
560 except:
561 s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
562 info = s
563 shutil.copy(ref_file_name,fakefasta)
564 pic.delme.append(fakefasta)
565 x = 'rgPicardGCBiasMetrics'
566 pdfname = '%s.pdf' % x
567 jpgname = '%s.jpg' % x
568 tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out')
569 temppdf = os.path.join(opts.outdir,pdfname)
570 cl.append('R=%s' % fakefasta)
571 cl.append('WINDOW_SIZE=%s' % opts.windowsize)
572 cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac)
573 cl.append('INPUT=%s' % opts.input)
574 cl.append('OUTPUT=%s' % tempout)
575 cl.append('TMP_DIR=%s' % opts.tmpdir)
576 cl.append('CHART_OUTPUT=%s' % temppdf)
577 cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
578 pic.runPic(opts.jar,cl)
579 if os.path.isfile(temppdf):
580 cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
581 s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir)
582 else:
583 s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
584 lf = open(pic.log_filename,'a')
585 lf.write(s)
586 lf.write('\n')
587 lf.close()
588
589 elif pic.picname == 'CollectInsertSizeMetrics':
590 isPDF = 'InsertSizeHist.pdf'
591 pdfpath = os.path.join(opts.outdir,isPDF)
592 histpdf = 'InsertSizeHist.pdf'
593 cl.append('I=%s' % opts.input)
594 cl.append('O=%s' % pic.metricsOut)
595 cl.append('HISTOGRAM_FILE=%s' % histpdf)
596 if opts.taillimit <> '0':
597 cl.append('TAIL_LIMIT=%s' % opts.taillimit)
598 if opts.histwidth <> '0':
599 cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
600 if float( opts.minpct) > 0.0:
601 cl.append('MINIMUM_PCT=%s' % opts.minpct)
602 pic.runPic(opts.jar,cl)
603 if os.path.exists(pdfpath): # automake thumbnail - will be added to html
604 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
605 s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir)
606 else:
607 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
608 s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
609 s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
610 s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
611 stdouts = ''
612 logging.info(s)
613 if len(stdouts) > 0:
614 logging.info(stdouts)
615
616 elif pic.picname == 'MarkDuplicates':
617 # assume sorted even if header says otherwise
618 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
619 # input
620 cl.append('INPUT=%s' % opts.input)
621 # outputs
622 cl.append('OUTPUT=%s' % opts.output)
623 cl.append('METRICS_FILE=%s' % pic.metricsOut )
624 # remove or mark duplicates
625 cl.append('REMOVE_DUPLICATES=%s' % opts.remdups)
626 # the regular expression to be used to parse reads in incoming SAM file
627 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
628 # maximum offset between two duplicate clusters
629 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
630 pic.runPic(opts.jar, cl)
631
632 elif pic.picname == 'FixMateInformation':
633 cl.append('I=%s' % opts.input)
634 cl.append('O=%s' % tempout)
635 cl.append('SORT_ORDER=%s' % opts.sortorder)
636 pic.runPic(opts.jar,cl)
637 haveTempout = True
638
639 elif pic.picname == 'ReorderSam':
640 # input
641 cl.append('INPUT=%s' % opts.input)
642 # output
643 cl.append('OUTPUT=%s' % tempout)
644 # reference
645 cl.append('REFERENCE=%s' % ref_file_name)
646 # incomplete dict concordance
647 if opts.allow_inc_dict_concord == 'true':
648 cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true')
649 # contig length discordance
650 if opts.allow_contig_len_discord == 'true':
651 cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
652 pic.runPic(opts.jar, cl)
653 haveTempout = True
654
655 elif pic.picname == 'ReplaceSamHeader':
656 cl.append('INPUT=%s' % opts.input)
657 cl.append('OUTPUT=%s' % tempout)
658 cl.append('HEADER=%s' % opts.header_file)
659 pic.runPic(opts.jar, cl)
660 haveTempout = True
661
662 elif pic.picname == 'CalculateHsMetrics':
663 maxloglines = 100
664 baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait')
665 targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target')
666 baitf = pic.makePicInterval(opts.baitbed,baitfname)
667 if opts.targetbed == opts.baitbed: # same file sometimes
668 targetf = baitf
669 else:
670 targetf = pic.makePicInterval(opts.targetbed,targetfname)
671 cl.append('BAIT_INTERVALS=%s' % baitf)
672 cl.append('TARGET_INTERVALS=%s' % targetf)
673 cl.append('INPUT=%s' % os.path.abspath(opts.input))
674 cl.append('OUTPUT=%s' % pic.metricsOut)
675 cl.append('TMP_DIR=%s' % opts.tmpdir)
676 pic.runPic(opts.jar,cl)
677
678 elif pic.picname == 'ValidateSamFile':
679 import pysam
680 doTranspose = False
681 sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
682 stf = open(pic.log_filename,'w')
683 tlog = None
684 if opts.datatype == 'sam': # need to work with a bam
685 tlog,tempbam = pic.samToBam(opts.input,opts.outdir)
686 try:
687 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
688 except:
689 print '## exception on sorting sam file %s' % opts.input
690 else: # is already bam
691 try:
692 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
693 except: # bug - [bam_sort_core] not being ignored - TODO fixme
694 print '## exception on sorting bam file %s' % opts.input
695 if tlog:
696 print '##tlog=',tlog
697 stf.write(tlog)
698 stf.write('\n')
699 sortedfile = '%s.bam' % sortedfile # samtools does that
700 cl.append('O=%s' % pic.metricsOut)
701 cl.append('TMP_DIR=%s' % opts.tmpdir)
702 cl.append('I=%s' % sortedfile)
703 opts.maxerrors = '99999999'
704 cl.append('MAX_OUTPUT=%s' % opts.maxerrors)
705 if opts.ignoreflags[0] <> 'None': # picard error values to ignore
706 igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None']
707 cl.append(' '.join(igs))
708 if opts.bisulphite.lower() <> 'false':
709 cl.append('IS_BISULFITE_SEQUENCED=true')
710 if opts.ref <> None or opts.ref_file <> None:
711 cl.append('R=%s' % ref_file_name)
712 pic.runPic(opts.jar,cl)
713 if opts.datatype == 'sam':
714 pic.delme.append(tempbam)
715 newsam = opts.output
716 outformat = 'bam'
717 pe = open(pic.metricsOut,'r').readlines()
718 pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)
719 pic.delme.append(sortedfile) # not wanted
720 stf.close()
721 pic.cleanup()
722 else:
723 print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname
724 sys.exit(1)
725 if haveTempout:
726 # Some Picard tools produced a potentially intermediate bam file.
727 # Either just move to final location or create sam
728 shutil.move(tempout, os.path.abspath(opts.output))
729
730 if opts.htmlout <> None or doFix: # return a pretty html page
731 pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
732
733 if __name__=="__main__": __main__()
734