Mercurial > repos > devteam > picard1106
annotate picard_wrapper.py @ 146:767bcb0a06df draft
fixed downsamplesam
author | Rayan Chikhi <chikhi@psu.edu> |
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date | Mon, 21 Jul 2014 15:24:40 -0400 |
parents | b2ca2d181fb4 |
children |
rev | line source |
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135 | 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( 'Read Large Exception : %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 rval > 0: | |
129 s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs) | |
130 stdouts = '%s\n%s' % (stdouts,stderrs) | |
131 else: | |
132 s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval) | |
133 logging.info(s) | |
134 os.unlink(templog) # always | |
135 os.unlink(temperr) # always | |
136 return s, stdouts, rval # sometimes s is an output | |
137 | |
138 def runPic(self, jar, cl): | |
139 """ | |
140 cl should be everything after the jar file name in the command | |
141 """ | |
142 runme = ['java -Xmx%s' % self.opts.maxjheap] | |
143 runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir) | |
144 runme.append('-jar %s' % jar) | |
145 runme += cl | |
146 s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir) | |
147 return stdouts,rval | |
148 | |
149 def samToBam(self,infile=None,outdir=None): | |
150 """ | |
151 use samtools view to convert sam to bam | |
152 """ | |
153 fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam') | |
154 cl = ['samtools view -h -b -S -o ',tempbam,infile] | |
155 tlog,stdouts,rval = self.runCL(cl,outdir) | |
156 return tlog,tempbam,rval | |
157 | |
158 def sortSam(self, infile=None,outfile=None,outdir=None): | |
159 """ | |
160 """ | |
161 print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir) | |
162 cl = ['samtools sort',infile,outfile] | |
163 tlog,stdouts,rval = self.runCL(cl,outdir) | |
164 return tlog | |
165 | |
166 def cleanup(self): | |
167 for fname in self.delme: | |
168 try: | |
169 os.unlink(fname) | |
170 except: | |
171 pass | |
172 | |
173 def prettyPicout(self,transpose,maxrows): | |
174 """organize picard outpouts into a report html page | |
175 """ | |
176 res = [] | |
177 try: | |
178 r = open(self.metricsOut,'r').readlines() | |
179 except: | |
180 r = [] | |
181 if len(r) > 0: | |
182 res.append('<b>Picard on line resources</b><ul>\n') | |
183 res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n') | |
184 res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n') | |
185 if transpose: | |
186 res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n') | |
187 else: | |
188 res.append('<b>Picard output</b><hr/>\n') | |
189 res.append('<table cellpadding="3" >\n') | |
190 dat = [] | |
191 heads = [] | |
192 lastr = len(r) - 1 | |
193 # special case for estimate library complexity hist | |
194 thist = False | |
195 for i,row in enumerate(r): | |
196 if row.strip() > '': | |
197 srow = row.split('\t') | |
198 if row.startswith('#'): | |
199 heads.append(row.strip()) # want strings | |
200 else: | |
201 dat.append(srow) # want lists | |
202 if row.startswith('## HISTOGRAM'): | |
203 thist = True | |
204 if len(heads) > 0: | |
205 hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)] | |
206 res += hres | |
207 heads = [] | |
208 if len(dat) > 0: | |
209 if transpose and not thist: | |
210 tdat = map(None,*dat) # transpose an arbitrary list of lists | |
211 tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)] | |
212 else: | |
213 tdat = ['\t'.join(x).strip() for x in dat] # back to strings :( | |
214 tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)] | |
215 res += tdat | |
216 dat = [] | |
217 res.append('</table>\n') | |
218 return res | |
219 | |
220 def fixPicardOutputs(self,transpose,maxloglines): | |
221 """ | |
222 picard produces long hard to read tab header files | |
223 make them available but present them transposed for readability | |
224 """ | |
225 logging.shutdown() | |
226 self.cleanup() # remove temp files stored in delme | |
227 rstyle="""<style type="text/css"> | |
228 tr.d0 td {background-color: oldlace; color: black;} | |
229 tr.d1 td {background-color: aliceblue; color: black;} | |
230 </style>""" | |
231 res = [rstyle,] | |
232 res.append(galhtmlprefix % self.progname) | |
233 res.append(galhtmlattr % (self.picname,timenow())) | |
234 flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')] | |
235 pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] | |
236 if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs | |
237 for p in pdflist: | |
238 pbase = os.path.splitext(p)[0] # removes .pdf | |
239 imghref = '%s.jpg' % pbase | |
240 mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking! | |
241 if mimghref in flist: | |
242 imghref=mimghref # only one for thumbnail...it's a multi page pdf | |
243 res.append('<table cellpadding="10"><tr><td>\n') | |
244 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)) | |
245 res.append('</tr></td></table>\n') | |
246 if len(flist) > 0: | |
247 res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>') | |
248 res.append('<table>\n') | |
249 for i,f in enumerate(flist): | |
250 fn = os.path.split(f)[-1] | |
251 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn)) | |
252 res.append('</table><p/>\n') | |
253 pres = self.prettyPicout(transpose,maxloglines) | |
254 if len(pres) > 0: | |
255 res += pres | |
256 l = open(self.log_filename,'r').readlines() | |
257 llen = len(l) | |
258 if llen > 0: | |
259 res.append('<b>Picard Tool Run Log</b><hr/>\n') | |
260 rlog = ['<pre>',] | |
261 if llen > maxloglines: | |
262 n = min(50,int(maxloglines/2)) | |
263 rlog += l[:n] | |
264 rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines)) | |
265 rlog += l[-n:] | |
266 else: | |
267 rlog += l | |
268 rlog.append('</pre>') | |
269 if llen > maxloglines: | |
270 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)) | |
271 res += rlog | |
272 else: | |
273 res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename) | |
274 res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n') | |
275 res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool') | |
276 res.append(galhtmlpostfix) | |
277 outf = open(self.opts.htmlout,'w') | |
278 outf.write(''.join(res)) | |
279 outf.write('\n') | |
280 outf.close() | |
281 | |
282 def makePicInterval(self,inbed=None,outf=None): | |
283 """ | |
284 picard wants bait and target files to have the same header length as the incoming bam/sam | |
285 a meaningful (ie accurate) representation will fail because of this - so this hack | |
286 it would be far better to be able to supply the original bed untouched | |
287 Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list | |
288 """ | |
289 assert inbed <> None | |
290 bed = open(inbed,'r').readlines() | |
291 sbed = [x.split('\t') for x in bed] # lengths MUST be 5 | |
292 lens = [len(x) for x in sbed] | |
293 strands = [x[3] for x in sbed if not x[3] in ['+','-']] | |
294 maxl = max(lens) | |
295 minl = min(lens) | |
296 e = [] | |
297 if maxl <> minl: | |
298 e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed) | |
299 if maxl <> 5: | |
300 e.append("## Input error: %d fields found in %s, 5 required - please read the warning and documentation on bait/target format requirements, fix and try again" % (maxl,inbed)) | |
301 if len(strands) > 0: | |
302 e.append("## Input error: Fourth column in %s is not the required strand (+ or -) - please read the warning and documentation on bait/target format requirements, fix and try again" % (inbed)) | |
303 if len(e) > 0: # write to stderr and quit | |
304 print >> sys.stderr, '\n'.join(e) | |
305 sys.exit(1) | |
306 thead = os.path.join(self.opts.outdir,'tempSamHead.txt') | |
307 if self.opts.datatype == 'sam': | |
308 cl = ['samtools view -H -S',self.opts.input,'>',thead] | |
309 else: | |
310 cl = ['samtools view -H',self.opts.input,'>',thead] | |
311 self.runCL(cl=cl,output_dir=self.opts.outdir) | |
312 head = open(thead,'r').readlines() | |
313 s = '## got %d rows of header\n' % (len(head)) | |
314 logging.info(s) | |
315 o = open(outf,'w') | |
316 o.write(''.join(head)) | |
317 o.write(''.join(bed)) | |
318 o.close() | |
319 return outf | |
320 | |
321 def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None): | |
322 """ | |
323 interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs! | |
324 Do the work of removing all the error sequences | |
325 pysam is cool | |
326 infile = pysam.Samfile( "-", "r" ) | |
327 outfile = pysam.Samfile( "-", "w", template = infile ) | |
328 for s in infile: outfile.write(s) | |
329 | |
330 errors from ValidateSameFile.jar look like | |
331 WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing | |
332 ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary. | |
333 ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041 | |
334 | |
335 """ | |
336 assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam | |
337 assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path' | |
338 removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2] | |
339 remDict = dict(zip(removeNames,range(len(removeNames)))) | |
340 infile = pysam.Samfile(insam,'rb') | |
341 info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict)) | |
342 if len(removeNames) > 0: | |
343 outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file | |
344 i = 0 | |
345 j = 0 | |
346 for row in infile: | |
347 dropme = remDict.get(row.qname,None) # keep if None | |
348 if not dropme: | |
349 outfile.write(row) | |
350 j += 1 | |
351 else: # discard | |
352 i += 1 | |
353 info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam)) | |
354 outfile.close() | |
355 infile.close() | |
356 else: # we really want a nullop or a simple pointer copy | |
357 infile.close() | |
358 if newsam: | |
359 shutil.copy(insam,newsam) | |
360 logging.info(info) | |
361 | |
362 | |
363 | |
364 def __main__(): | |
365 doFix = False # tools returning htmlfile don't need this | |
366 doTranspose = True # default | |
367 maxloglines = 100 # default | |
368 #Parse Command Line | |
369 op = optparse.OptionParser() | |
370 # All tools | |
371 op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' ) | |
372 op.add_option('-e', '--inputext', default=None) | |
373 op.add_option('-o', '--output', default=None) | |
374 op.add_option('-n', '--title', default="Pick a Picard Tool") | |
375 op.add_option('-t', '--htmlout', default=None) | |
376 op.add_option('-d', '--outdir', default=None) | |
377 op.add_option('-x', '--maxjheap', default='3000m') | |
378 op.add_option('-b', '--bisulphite', default='false') | |
379 op.add_option('-s', '--sortorder', default='query') | |
380 op.add_option('','--tmpdir', default='/tmp') | |
381 op.add_option('-j','--jar',default='') | |
382 op.add_option('','--picard-cmd',default=None) | |
383 # Many tools | |
384 op.add_option( '', '--output-format', dest='output_format', help='Output format' ) | |
385 op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' ) | |
386 op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None ) | |
387 # CreateSequenceDictionary | |
388 op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None ) | |
389 op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' ) | |
390 op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' ) | |
391 op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' ) | |
392 # MarkDuplicates | |
393 op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' ) | |
394 op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' ) | |
395 # CollectInsertSizeMetrics | |
396 op.add_option('', '--taillimit', default="0") | |
397 op.add_option('', '--histwidth', default="0") | |
398 op.add_option('', '--minpct', default="0.01") | |
399 op.add_option('', '--malevel', default='') | |
400 op.add_option('', '--deviations', default="0.0") | |
401 # CollectAlignmentSummaryMetrics | |
402 op.add_option('', '--maxinsert', default="20") | |
403 op.add_option('', '--adaptors', default='') | |
404 # FixMateInformation and validate | |
405 # CollectGcBiasMetrics | |
406 op.add_option('', '--windowsize', default='100') | |
407 op.add_option('', '--mingenomefrac', default='0.00001') | |
408 # AddOrReplaceReadGroups | |
409 op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' ) | |
410 op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' ) | |
411 op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' ) | |
412 op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' ) | |
413 op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' ) | |
414 op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' ) | |
415 op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' ) | |
416 op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' ) | |
417 # ReorderSam | |
418 op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' ) | |
419 op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' ) | |
420 # ReplaceSamHeader | |
421 op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' ) | |
422 | |
423 op.add_option('','--assumesorted', default='true') | |
424 op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*") | |
425 #estimatelibrarycomplexity | |
426 op.add_option('','--minid', default="5") | |
427 op.add_option('','--maxdiff', default="0.03") | |
428 op.add_option('','--minmeanq', default="20") | |
429 #hsmetrics | |
430 op.add_option('','--baitbed', default=None) | |
431 op.add_option('','--targetbed', default=None) | |
432 #validate | |
433 op.add_option('','--ignoreflags', action='append', type="string") | |
434 op.add_option('','--maxerrors', default=None) | |
435 op.add_option('','--datatype', default=None) | |
436 op.add_option('','--bamout', default=None) | |
437 op.add_option('','--samout', default=None) | |
438 #downsample | |
439 op.add_option('','--probability', default="1") | |
440 op.add_option('','--seed', default="1") | |
441 #meanqualitybycycle | |
442 op.add_option('','--pfreadsonly', default='false') | |
443 op.add_option('','--alignedreadsonly', default='false') | |
444 #collectrnaseqmetrics | |
445 op.add_option('','--ignoreseq', action='append', type="string") | |
446 op.add_option('','--minlength', default=None) | |
447 op.add_option('','--refflat', default=None) | |
448 op.add_option('','--strandspecificity', default=None) | |
449 op.add_option('','--ribosomalintervals', default='null') | |
450 op.add_option('','--rrnafragmentpercentage', default=None) | |
451 | |
452 opts, args = op.parse_args() | |
453 opts.sortme = opts.assumesorted == 'false' | |
454 assert opts.input <> None | |
455 # need to add | |
456 # instance that does all the work | |
457 pic = PicardBase(opts,sys.argv[0]) | |
458 | |
459 tmp_dir = opts.outdir | |
460 haveTempout = False # we use this where sam output is an option | |
461 rval = 0 | |
462 stdouts = 'Not run yet' | |
463 # set ref and dict files to use (create if necessary) | |
464 ref_file_name = opts.ref | |
465 if opts.ref_file <> None: | |
466 csd = 'CreateSequenceDictionary' | |
467 realjarpath = os.path.split(opts.jar)[0] | |
468 jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq | |
469 tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname) | |
470 ref_file_name = '%s.fasta' % tmp_ref_name | |
471 # build dict | |
472 dict_file_name = '%s.dict' % tmp_ref_name | |
473 os.symlink( opts.ref_file, ref_file_name ) | |
474 cl = ['REFERENCE=%s' % ref_file_name] | |
475 cl.append('OUTPUT=%s' % dict_file_name) | |
476 cl.append('URI=%s' % os.path.basename( opts.ref_file )) | |
477 cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names) | |
478 if opts.species_name: | |
479 cl.append('SPECIES=%s' % opts.species_name) | |
480 if opts.build_name: | |
481 cl.append('GENOME_ASSEMBLY=%s' % opts.build_name) | |
482 pic.delme.append(dict_file_name) | |
483 pic.delme.append(ref_file_name) | |
484 pic.delme.append(tmp_ref_name) | |
485 stdouts,rval = pic.runPic(jarpath, cl) | |
486 # run relevant command(s) | |
487 | |
488 # define temporary output | |
489 # if output is sam, it must have that extension, otherwise bam will be produced | |
490 # specify sam or bam file with extension | |
491 if opts.output_format == 'sam': | |
492 suff = '.sam' | |
493 else: | |
494 suff = '' | |
495 tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff ) | |
496 | |
497 cl = ['VALIDATION_STRINGENCY=LENIENT',] | |
498 | |
499 if pic.picname == 'AddOrReplaceReadGroups': | |
500 # sort order to match Galaxy's default | |
501 cl.append('SORT_ORDER=coordinate') | |
502 # input | |
503 cl.append('INPUT=%s' % opts.input) | |
504 # outputs | |
505 cl.append('OUTPUT=%s' % tempout) | |
506 # required read groups | |
507 cl.append('RGLB="%s"' % opts.rg_library) | |
508 cl.append('RGPL="%s"' % opts.rg_platform) | |
509 cl.append('RGPU="%s"' % opts.rg_plat_unit) | |
510 cl.append('RGSM="%s"' % opts.rg_sample) | |
511 if opts.rg_id: | |
512 cl.append('RGID="%s"' % opts.rg_id) | |
513 # optional read groups | |
514 if opts.rg_seq_center: | |
515 cl.append('RGCN="%s"' % opts.rg_seq_center) | |
516 if opts.rg_desc: | |
517 cl.append('RGDS="%s"' % opts.rg_desc) | |
518 stdouts,rval = pic.runPic(opts.jar, cl) | |
519 haveTempout = True | |
520 | |
521 elif pic.picname == 'BamIndexStats': | |
522 tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir ) | |
523 tmp_bam_name = '%s.bam' % tmp_name | |
524 tmp_bai_name = '%s.bai' % tmp_bam_name | |
525 os.symlink( opts.input, tmp_bam_name ) | |
526 os.symlink( opts.bai_file, tmp_bai_name ) | |
527 cl.append('INPUT=%s' % ( tmp_bam_name )) | |
528 pic.delme.append(tmp_bam_name) | |
529 pic.delme.append(tmp_bai_name) | |
530 pic.delme.append(tmp_name) | |
531 stdouts,rval = pic.runPic( opts.jar, cl ) | |
532 f = open(pic.metricsOut,'a') | |
533 f.write(stdouts) # got this on stdout from runCl | |
534 f.write('\n') | |
535 f.close() | |
536 doTranspose = False # but not transposed | |
537 | |
538 elif pic.picname == 'EstimateLibraryComplexity': | |
539 cl.append('I=%s' % opts.input) | |
540 cl.append('O=%s' % pic.metricsOut) | |
541 if float(opts.minid) > 0: | |
542 cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid) | |
543 if float(opts.maxdiff) > 0.0: | |
544 cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff) | |
545 if float(opts.minmeanq) > 0: | |
546 cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq) | |
547 if opts.readregex > '': | |
548 cl.append('READ_NAME_REGEX="%s"' % opts.readregex) | |
549 if float(opts.optdupdist) > 0: | |
550 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) | |
551 stdouts,rval = pic.runPic(opts.jar, cl) | |
552 | |
553 elif pic.picname == 'CollectAlignmentSummaryMetrics': | |
554 # Why do we do this fakefasta thing? | |
555 # Because we need NO fai to be available or picard barfs unless it matches the input data. | |
556 # why? Dunno Seems to work without complaining if the .bai file is AWOL.... | |
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? Will shutil.copy' | |
562 info = s | |
563 shutil.copy(ref_file_name,fakefasta) | |
564 pic.delme.append(fakefasta) | |
565 cl.append('ASSUME_SORTED=true') | |
566 adaptlist = opts.adaptors.split(',') | |
567 adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist] | |
568 cl += adaptorseqs | |
569 cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite) | |
570 cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert) | |
571 cl.append('OUTPUT=%s' % pic.metricsOut) | |
572 cl.append('R=%s' % fakefasta) | |
573 cl.append('TMP_DIR=%s' % opts.tmpdir) | |
574 if not opts.assumesorted.lower() == 'true': # we need to sort input | |
575 sortedfile = '%s.sorted' % os.path.basename(opts.input) | |
576 if opts.datatype == 'sam': # need to work with a bam | |
577 tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir) | |
578 pic.delme.append(tempbam) | |
579 try: | |
580 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) | |
581 except: | |
582 print '## exception on sorting sam file %s' % opts.input | |
583 else: # is already bam | |
584 try: | |
585 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) | |
586 except : # bug - [bam_sort_core] not being ignored - TODO fixme | |
587 print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input) | |
588 cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile))) | |
589 pic.delme.append(os.path.join(opts.outdir,sortedfile)) | |
590 else: | |
591 cl.append('INPUT=%s' % os.path.abspath(opts.input)) | |
592 stdouts,rval = pic.runPic(opts.jar, cl) | |
593 | |
594 | |
595 elif pic.picname == 'CollectGcBiasMetrics': | |
596 assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name | |
597 # 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. | |
598 # why? Dunno | |
599 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) | |
600 try: | |
601 os.symlink(ref_file_name,fakefasta) | |
602 except: | |
603 s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' | |
604 info = s | |
605 shutil.copy(ref_file_name,fakefasta) | |
606 pic.delme.append(fakefasta) | |
607 x = 'rgPicardGCBiasMetrics' | |
608 pdfname = '%s.pdf' % x | |
609 jpgname = '%s.jpg' % x | |
610 tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out') | |
611 temppdf = os.path.join(opts.outdir,pdfname) | |
612 cl.append('R=%s' % fakefasta) | |
613 cl.append('WINDOW_SIZE=%s' % opts.windowsize) | |
614 cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) | |
615 cl.append('INPUT=%s' % opts.input) | |
616 cl.append('OUTPUT=%s' % tempout) | |
617 cl.append('TMP_DIR=%s' % opts.tmpdir) | |
618 cl.append('CHART_OUTPUT=%s' % temppdf) | |
619 cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut) | |
620 stdouts,rval = pic.runPic(opts.jar, cl) | |
621 if os.path.isfile(temppdf): | |
622 cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find | |
623 s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir) | |
624 else: | |
625 s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf | |
626 lf = open(pic.log_filename,'a') | |
627 lf.write(s) | |
628 lf.write('\n') | |
629 lf.close() | |
630 | |
631 elif pic.picname == 'CollectInsertSizeMetrics': | |
632 """ <command interpreter="python"> | |
633 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" | |
634 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" | |
635 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" | |
636 </command> | |
637 """ | |
638 isPDF = 'InsertSizeHist.pdf' | |
639 pdfpath = os.path.join(opts.outdir,isPDF) | |
640 histpdf = 'InsertSizeHist.pdf' | |
641 cl.append('I=%s' % opts.input) | |
642 cl.append('O=%s' % pic.metricsOut) | |
643 cl.append('HISTOGRAM_FILE=%s' % histpdf) | |
644 #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56 | |
645 # cl.append('TAIL_LIMIT=%s' % opts.taillimit) | |
646 if opts.histwidth <> '0': | |
647 cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth) | |
648 if float( opts.minpct) > 0.0: | |
649 cl.append('MINIMUM_PCT=%s' % opts.minpct) | |
650 if float(opts.deviations) > 0.0: | |
651 cl.append('DEVIATIONS=%s' % opts.deviations) | |
652 if opts.malevel: | |
653 malists = opts.malevel.split(',') | |
654 malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] | |
655 cl += malist | |
656 stdouts,rval = pic.runPic(opts.jar, cl) | |
657 if os.path.exists(pdfpath): # automake thumbnail - will be added to html | |
658 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] | |
659 pic.runCL(cl=cl2,output_dir=opts.outdir) | |
660 else: | |
661 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath | |
662 s += 'This <b>always happens if single ended data was provided</b> to this tool,\n' | |
663 s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' | |
664 s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' | |
665 logging.info(s) | |
666 if len(stdouts) > 0: | |
667 logging.info(stdouts) | |
668 | |
669 elif pic.picname == 'MarkDuplicates': | |
670 # assume sorted even if header says otherwise | |
671 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) | |
672 # input | |
673 cl.append('INPUT=%s' % opts.input) | |
674 # outputs | |
675 cl.append('OUTPUT=%s' % opts.output) | |
676 cl.append('METRICS_FILE=%s' % pic.metricsOut ) | |
677 # remove or mark duplicates | |
678 cl.append('REMOVE_DUPLICATES=%s' % opts.remdups) | |
679 # the regular expression to be used to parse reads in incoming SAM file | |
680 cl.append('READ_NAME_REGEX="%s"' % opts.readregex) | |
681 # maximum offset between two duplicate clusters | |
682 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) | |
683 stdouts,rval = pic.runPic(opts.jar, cl) | |
684 | |
685 elif pic.picname == 'FixMateInformation': | |
686 cl.append('I=%s' % opts.input) | |
687 cl.append('O=%s' % tempout) | |
688 cl.append('SORT_ORDER=%s' % opts.sortorder) | |
689 stdouts,rval = pic.runPic(opts.jar,cl) | |
690 haveTempout = True | |
691 | |
692 elif pic.picname == 'ReorderSam': | |
693 # input | |
694 cl.append('INPUT=%s' % opts.input) | |
695 # output | |
696 cl.append('OUTPUT=%s' % tempout) | |
697 # reference | |
698 cl.append('REFERENCE=%s' % ref_file_name) | |
699 # incomplete dict concordance | |
700 if opts.allow_inc_dict_concord == 'true': | |
701 cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true') | |
702 # contig length discordance | |
703 if opts.allow_contig_len_discord == 'true': | |
704 cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') | |
705 stdouts,rval = pic.runPic(opts.jar, cl) | |
706 haveTempout = True | |
707 | |
708 elif pic.picname == 'ReplaceSamHeader': | |
709 cl.append('INPUT=%s' % opts.input) | |
710 cl.append('OUTPUT=%s' % tempout) | |
711 cl.append('HEADER=%s' % opts.header_file) | |
712 stdouts,rval = pic.runPic(opts.jar, cl) | |
713 haveTempout = True | |
714 | |
715 elif pic.picname == 'CalculateHsMetrics': | |
716 maxloglines = 100 | |
717 baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait') | |
718 targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target') | |
719 baitf = pic.makePicInterval(opts.baitbed,baitfname) | |
720 if opts.targetbed == opts.baitbed: # same file sometimes | |
721 targetf = baitf | |
722 else: | |
723 targetf = pic.makePicInterval(opts.targetbed,targetfname) | |
724 cl.append('BAIT_INTERVALS=%s' % baitf) | |
725 cl.append('TARGET_INTERVALS=%s' % targetf) | |
726 cl.append('INPUT=%s' % os.path.abspath(opts.input)) | |
727 cl.append('OUTPUT=%s' % pic.metricsOut) | |
728 cl.append('TMP_DIR=%s' % opts.tmpdir) | |
729 stdouts,rval = pic.runPic(opts.jar,cl) | |
730 | |
731 elif pic.picname == 'ValidateSamFile': | |
732 import pysam | |
733 doTranspose = False | |
734 sortedfile = os.path.join(opts.outdir,'rgValidate.sorted') | |
735 stf = open(pic.log_filename,'w') | |
736 tlog = None | |
737 if opts.datatype == 'sam': # need to work with a bam | |
738 tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) | |
739 try: | |
740 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) | |
741 except: | |
742 print '## exception on sorting sam file %s' % opts.input | |
743 else: # is already bam | |
744 try: | |
745 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) | |
746 except: # bug - [bam_sort_core] not being ignored - TODO fixme | |
747 print '## exception on sorting bam file %s' % opts.input | |
748 if tlog: | |
749 print '##tlog=',tlog | |
750 stf.write(tlog) | |
751 stf.write('\n') | |
752 sortedfile = '%s.bam' % sortedfile # samtools does that | |
753 cl.append('O=%s' % pic.metricsOut) | |
754 cl.append('TMP_DIR=%s' % opts.tmpdir) | |
755 cl.append('I=%s' % sortedfile) | |
756 opts.maxerrors = '99999999' | |
757 cl.append('MAX_OUTPUT=%s' % opts.maxerrors) | |
758 if opts.ignoreflags[0] <> 'None': # picard error values to ignore | |
759 igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None'] | |
760 cl.append(' '.join(igs)) | |
761 if opts.bisulphite.lower() <> 'false': | |
762 cl.append('IS_BISULFITE_SEQUENCED=true') | |
763 if opts.ref <> None or opts.ref_file <> None: | |
764 cl.append('R=%s' % ref_file_name) | |
765 stdouts,rval = pic.runPic(opts.jar,cl) | |
766 if opts.datatype == 'sam': | |
767 pic.delme.append(tempbam) | |
768 newsam = opts.output | |
769 outformat = 'bam' | |
770 pe = open(pic.metricsOut,'r').readlines() | |
771 pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat) | |
772 pic.delme.append(sortedfile) # not wanted | |
773 stf.close() | |
774 pic.cleanup() | |
775 | |
776 ####liubo added CleanSam tool#### | |
777 elif pic.picname == 'CleanSam': | |
778 # input | |
779 cl.append('INPUT=%s' % opts.input) | |
780 # output | |
781 cl.append('OUTPUT=%s' % tempout) | |
782 stdouts,rval = pic.runPic(opts.jar, cl) | |
783 haveTempout = True | |
784 | |
785 elif pic.picname == 'SortSam': | |
786 cl.append('I=%s' % opts.input) | |
787 cl.append('O=%s' % tempout) | |
788 cl.append('SORT_ORDER=%s' % opts.sortorder) | |
789 stdouts,rval = pic.runPic(opts.jar,cl) | |
790 haveTempout = True | |
791 | |
792 elif pic.picname == 'BuildBamIndex': | |
793 cl.append('I=%s' % opts.input) | |
794 cl.append('O=%s' % tempout) | |
795 stdouts,rval = pic.runPic(opts.jar,cl) | |
796 haveTempout = True | |
797 | |
798 elif pic.picname == 'SamFormatConverter': | |
799 cl.append('INPUT=%s' % opts.input) | |
800 cl.append('OUTPUT=%s' % tempout) | |
801 pic.runPic(opts.jar, cl) | |
802 haveTempout = True | |
143
b2ca2d181fb4
fixed downsample sam in picard1106 (accept bam)
Rayan Chikhi <chikhi@psu.edu>
parents:
135
diff
changeset
|
803 |
135 | 804 elif pic.picname == "DownsampleSam": |
805 cl.append('I=%s' % opts.input) | |
143
b2ca2d181fb4
fixed downsample sam in picard1106 (accept bam)
Rayan Chikhi <chikhi@psu.edu>
parents:
135
diff
changeset
|
806 output_string = opts.output |
146 | 807 if opts.output_format == 'sam': |
143
b2ca2d181fb4
fixed downsample sam in picard1106 (accept bam)
Rayan Chikhi <chikhi@psu.edu>
parents:
135
diff
changeset
|
808 output_string = output_string + ".sam" |
b2ca2d181fb4
fixed downsample sam in picard1106 (accept bam)
Rayan Chikhi <chikhi@psu.edu>
parents:
135
diff
changeset
|
809 cl.append('O=%s' % output_string) |
135 | 810 if float(opts.probability) > 0: |
811 cl.append('PROBABILITY=%s' % opts.probability) | |
812 if float(opts.seed) > 0: | |
813 cl.append('RANDOM_SEED=%s' % opts.seed) | |
814 stdouts,rval = pic.runPic(opts.jar, cl) | |
146 | 815 if opts.output_format == 'sam': |
816 os.rename(output_string, opts.output) | |
135 | 817 |
818 elif pic.picname == 'MeanQualityByCycle': | |
819 isPDF = 'MeanQualityByCycle.pdf' | |
820 pdfpath = os.path.join(opts.outdir,isPDF) | |
821 histpdf = isPDF | |
822 cl.append('I=%s' % opts.input) | |
823 cl.append('O=%s' % pic.metricsOut) | |
824 cl.append('CHART_OUTPUT=%s' % histpdf) | |
825 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) | |
826 cl.append('ALIGNED_READS_ONLY=%s' % (opts.alignedreadsonly)) | |
827 cl.append('PF_READS_ONLY=%s' % (opts.pfreadsonly)) | |
828 stdouts,rval = pic.runPic(opts.jar, cl) | |
829 if os.path.exists(pdfpath): # automake thumbnail - will be added to html | |
830 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] | |
831 pic.runCL(cl=cl2,output_dir=opts.outdir) | |
832 else: | |
833 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath | |
834 logging.info(s) | |
835 if len(stdouts) > 0: | |
836 logging.info(stdouts) | |
837 | |
838 elif pic.picname == 'CollectRnaSeqMetrics': | |
839 isPDF = pic.picname + '.pdf' | |
840 pdfpath = os.path.join(opts.outdir,isPDF) | |
841 histpdf = isPDF | |
842 cl.append('I=%s' % opts.input) | |
843 cl.append('O=%s' % pic.metricsOut) | |
844 cl.append('CHART_OUTPUT=%s' % histpdf) | |
845 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) | |
846 cl.append('MINIMUM_LENGTH=%s' % (opts.minlength)) | |
847 cl.append('REF_FLAT=%s' % (opts.refflat)) | |
848 cl.append('STRAND_SPECIFICITY=%s' % (opts.strandspecificity)) | |
849 cl.append('RIBOSOMAL_INTERVALS=%s' % (opts.ribosomalintervals)) | |
850 cl.append('RRNA_FRAGMENT_PERCENTAGE=%s' % (opts.rrnafragmentpercentage)) | |
851 if opts.ignoreseq: # picard error values to ignore | |
852 igs = ['IGNORE_SEQUENCE=%s' % x for x in opts.ignoreseq if x <> 'None'] | |
853 cl.append(' '.join(igs)) | |
854 if opts.malevel: | |
855 malists = opts.malevel.split(',') | |
856 malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] | |
857 cl += malist | |
858 stdouts,rval = pic.runPic(opts.jar, cl) | |
859 if os.path.exists(pdfpath): # automake thumbnail - will be added to html | |
860 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] | |
861 pic.runCL(cl=cl2,output_dir=opts.outdir) | |
862 else: | |
863 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath | |
864 logging.info(s) | |
865 if len(stdouts) > 0: | |
866 logging.info(stdouts) | |
867 | |
868 else: | |
869 print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname | |
870 sys.exit(1) | |
871 if haveTempout: | |
872 # Some Picard tools produced a potentially intermediate bam file. | |
873 # Either just move to final location or create sam | |
874 if os.path.exists(tempout): | |
875 shutil.move(tempout, os.path.abspath(opts.output)) | |
876 if opts.htmlout <> None or doFix: # return a pretty html page | |
877 pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) | |
878 if rval <> 0: | |
879 print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts) | |
880 # signal failure | |
881 if __name__=="__main__": __main__() |