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comparison TEisotools-1.0/TEiso/LaunchTEiso.py @ 6:20ec0d14798e draft

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1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32
33
34 from commons.core.parsing.GtfParser import GtfParser
35 from commons.core.parsing.GffParser import GffParser
36 from TEiso.Bowtie_build import Bowtie_build
37 from TEiso.Tophat import Tophat
38 from TEiso.Cufflinks import Cufflinks
39 from TEiso.Cuffcompare import Cuffcompare
40 from TEiso.Bedtools_closest import Bedtools_closest
41 from commons.core.LoggerFactory import LoggerFactory
42 from commons.core.utils.RepetOptionParser import RepetOptionParser
43 from commons.core.utils.FileUtils import FileUtils
44 import os
45 import time
46 import re
47 import sys
48 LOG_NAME = "repet.TEiso"
49
50 class LaunchTEiso(object):
51
52 def __init__(self, reference="", input_transcripts="", single_paired="", single_reads="", left_reads="", right_reads="", transposable_element = "", assembly_tool="", verbosity=3):
53 self._reference = reference
54 self._transcripts = input_transcripts
55 self._type = single_paired
56 self._single_reads = single_reads.split(",")
57 self._left_reads = left_reads.split(",")
58 self._right_reads = right_reads.split(",")
59 self._TE = transposable_element
60 self._assembly_tool = assembly_tool
61 self._verbosity = verbosity
62 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_NAME, self.__class__.__name__), self._verbosity)
63
64 def _setAttributesFromCmdLine(self):
65 self._toolVersion = "0.1"
66 description = "TEiso version %s" % self._toolVersion
67 epilog = "\n if reads are single:\n LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e single -s <single_read> -t <TE.gff> -a cufflinks \n"
68 epilog += " if reads are paired:\n LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e paired -l <reads_left> -r <reads_right> -t <TE.gff> -a cufflinks \n"
69 parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion)
70 parser.add_option('-f' , '--input_reference' , dest='input_reference' , help='file with ref sequences')
71 parser.add_option('-g' , '--input_transcripts', dest='input_transcripts', help='GTF/GFF with known transcripts' , default="")
72 parser.add_option('-e' , '--single_paired' , dest='single_paired' , help='type of input reads, single or paired end', default="paired")
73 parser.add_option('-s' , '--single_read' , dest='single_read' , help='a single input read' , default="")
74 parser.add_option('-l', '--left_read' , dest='left_read' , help='left reads' , default="")
75 parser.add_option('-r', '--right_read' , dest='right_read' , help='right reads' , default="")
76 parser.add_option('-t' , '--input_transposable_element', dest='input_transposable_element', help='GFF with known transposable_element' , default="")
77 parser.add_option('-a' , '--assembly_tool' , dest='assembly_tool' , help='type of RNA-Seq assembly tool' , default="cufflinks")
78 options = parser.parse_args()[0]
79 self.setAttributesFromOptions(options)
80
81 def setAttributesFromOptions(self, options):
82 self._reference = options.input_reference
83 self._transcripts = options.input_transcripts
84 self._type = options.single_paired
85 self._single_reads = options.single_read.split(",")
86 self._left_reads = options.left_read.split(",")
87 self._right_reads = options.right_read.split(",")
88 self._TE = options.input_transposable_element
89 self._assembly_tool = options.assembly_tool
90
91 def _logAndRaise(self, errorMsg):
92 self._log.error(errorMsg)
93 #raise Exception(errorMsg)
94 sys.exit(1)
95
96 def checkOptions(self):
97 if self._type == "paired":
98 if self._single_reads != ['']:
99 self._logAndRaise("ERROR: for paired reads, you shoud use option left and right reads!")
100 if self._left_reads == ['']:
101 self._logAndRaise("ERROR: for paired reads, you shoud use option left and right reads!")
102 if self._right_reads == ['']:
103 self._logAndRaise("ERROR: for paired reads, you shoud use option left and right reads!")
104 if self._right_reads == self._left_reads:
105 self._logAndRaise("ERROR: -l and -r options are same!")
106
107 if self._type == "single":
108 if self._left_reads != ['']:
109 self._logAndRaise("ERROR: for single reads, you shoud use option single reads!")
110 if self._right_reads != ['']:
111 self._logAndRaise("ERROR: for single reads, you shoud use option single reads!")
112 if self._single_reads == ['']:
113 self._logAndRaise("ERROR: for single reads, you shoud use option single reads!")
114
115 if self._reference != "":
116 if not FileUtils.isRessourceExists(self._reference):
117 self._logAndRaise("ERROR: reference file %s does not exist!" % self._reference)
118 else:
119 self._logAndRaise("ERROR: No specified -f option!")
120
121 if self._transcripts != "":
122 if not FileUtils.isRessourceExists(self._transcripts):
123 self._logAndRaise("ERROR: transcripts file %s does not exist!" % self._transcripts)
124 else:
125 self._logAndRaise("ERROR: No specified -g option!")
126
127 if self._TE != "":
128 if not FileUtils.isRessourceExists(self._TE):
129 self._logAndRaise("ERROR: transposable elements %s does not exist!" % self._TE)
130 else:
131 self._logAndRaise("ERROR: No specified -t option!")
132
133
134
135 def getTranscriptToBed(self, inputFile,outputFile):
136 try:
137 filewrite=open(outputFile, "w")
138 gtfParser = GtfParser(inputFile, assemblyTools=True)
139 for transcript in gtfParser.getIterator():
140 if(transcript.getDirection()==1):
141 strand="+"
142 else:
143 strand="-"
144 filewrite.write("%s\t%s\t%s\t%s\t%s\t%s\t%.3f\n" % (transcript.getChromosome(),transcript.getStart(),
145 transcript.getEnd(), transcript.getTagValue("ID"), transcript.getTagValue("gene_id"),
146 strand,float(transcript.getTagValue("FPKM")) ))
147
148 filewrite.close()
149 except:
150 self._logAndRaise("Couldn't open %s for writing" % outputFile)
151
152
153 def getTEGFFToBed(self, inputFile, outputFile):
154 """TODO Dont write bed line when the strand is '.'
155 See Gtf parser option assemblyTools
156 """
157 try:
158 filewrite=open(outputFile, "w")
159 gffParser = GffParser(inputFile)
160 for transcript in gffParser.getIterator():
161 if(transcript.getDirection()==1):
162 strand="+"
163 else:
164 strand="-"
165 filewrite.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (transcript.getChromosome(),transcript.getStart(),
166 transcript.getEnd(), transcript.getTagValue("ID").split("_")[0]+"_", transcript.getTagValue("Target").split("_")[0], strand) )
167
168 filewrite.close()
169 except:
170 self._logAndRaise("Couldn't open %s for writing" % outputFile)
171
172
173 def getTEnearPromoter (self, bedtoolsfile):
174 #### BEdParser.py in commons is not used because the format of this bed file is different.
175 # #Chrom starttr endtr transcript_id gene_ID strand fpkm chromte startte endte idte targetTE strandTE distance
176 #scaffold_1 37570 37785 GSSPFG00034586001-RA GSSPFG00034586001 + 0.0000000000 scaffold_1 33914 40164 ms162_ PotentialHostGene - 0
177
178 linelist = []
179 tmplist = []
180 with open(bedtoolsfile, "r") as bedFile:
181 for line in bedFile.readlines():
182 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+([^\t]+)\t+([+-])\t+(\d+\.\d+)\t+([^\t]+)+\t+(\d+)\t+(\d+)\t+([^\t]+)+\t+([^\t]+)\t+([+-])\t+([^\t]+)",line)
183 if(m != None):
184 start_TR = int(m.group(2))##F[1]
185 end_TR = int(m.group(3))##F[2]
186 strand_TR= m.group(6) ##[5]
187 start_TE = int(m.group(9))##[8]
188 end_TE = int(m.group(10))##[9]
189 dist = int(m.group(14))##[13]
190 if (start_TE < start_TR) and (end_TE < start_TR) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE) and (dist != 0):
191 tmplist.append(line.strip())
192 tmplist.append("TE_closest_TSS")
193 linelist.append(tmplist)
194 tmplist = []
195 # F[1] gene F[2]
196 # =========================>
197 # ------------
198 # F[8] F[9]
199
200 if (start_TE > end_TR) and (end_TE > end_TR) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE) and (dist != 0):
201 tmplist.append(line.strip())
202 tmplist.append("TE_closest_TSS")
203 linelist.append(tmplist)
204 tmplist = []
205
206 # F[1] F[2]
207 # <======================
208 # ---------------
209
210 if (start_TE <= start_TR) and (start_TR < end_TE) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE):
211 for i in range(0,len(line.split("\t"))-1):
212 tmplist.append(line.split("\t")[i])
213 overlap = (end_TE-start_TR)+1
214 tmplist.append(overlap)
215 tmplist.append("TE_overlap_TSS")
216 linelist.append(tmplist)
217 tmplist = []
218
219 # F[1] gene F[2]
220 # =========================>
221 # -------------
222 # F[8] F[9]
223
224 # gene
225 # F[1]=========================>F[2]
226
227 # F[8]---------------F[9]
228
229
230 if (start_TE < start_TR) and (start_TR == end_TE) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE):
231 for i in range(0,len(line.split("\t"))-1):
232 tmplist.append(line.split("\t")[i])
233 tmplist.append(0)
234 tmplist.append("TE_overlap_TSS")
235 linelist.append(tmplist)
236 tmplist = []
237
238 ## F[1]=============================>F[2]
239 ## F[8]---------------F[9]
240
241
242 if (start_TE < end_TR) and (end_TR <= end_TE) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE):
243 for i in range(0,len(line.split("\t"))-1):
244 tmplist.append(line.split("\t")[i])
245 overlap = (end_TR-start_TE)+1
246 tmplist.append(overlap)
247 tmplist.append("TE_overlap_TSS")
248 linelist.append(tmplist)
249 tmplist = []
250
251
252 # F[1]<======================F[2]
253 # ---------------
254 # F[8] F[9]
255 #
256 #
257 # F[1]<=============================F[2]
258 # F[8]---------------F[9]
259
260 if (start_TE == end_TR) and (end_TR < end_TE) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE):
261 for i in range(0,len(line.split("\t"))-1):
262 tmplist.append(line.split("\t")[i])
263 tmplist.append(0)
264 tmplist.append("TE_overlap_TSS")
265 linelist.append(tmplist)
266 tmplist = []
267
268 # F[1]<=============================F[2]
269 # F[8]---------------F[9]
270
271 if (start_TR < start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE < end_TR) and (dist == 0):
272 tmplist.append(line.strip())
273 tmplist.append("TE_in_gene")
274 linelist.append(tmplist)
275 tmplist = []
276
277 # F[1] gene F[2]
278 # ==============================
279 # -----------
280 # F[8] F[9]
281
282
283 if (start_TE < start_TR) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TR < end_TE):
284 for i in range(0,len(line.split("\t"))-1):
285 tmplist.append(line.split("\t")[i])
286 lenTE = (end_TE-start_TE)+1
287 tmplist.append(lenTE)
288 tmplist.append("gene_in_TE")
289 linelist.append(tmplist)
290 tmplist = []
291
292 # F[1]======================F[2]
293 # F[8]----------------------------------------------------F[9]
294
295
296 if (strand_TR =="+") and (start_TR > start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE == end_TR):
297 tmplist.append(line.strip())
298 tmplist.append("gene_in_TE")
299 linelist.append(tmplist)
300 tmplist = []
301
302 # F[1]==================================>F[2]
303 # F[8]----------------------------------------------------------F[9]
304
305 if (strand_TR =="-") and (start_TR > start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE == end_TR):
306 tmplist.append(line.strip())
307 tmplist.append("gene_in_TE")
308 linelist.append(tmplist)
309 tmplist = []
310
311 # F[1]<==================================F[2]
312 # F[8]----------------------------------------------------------F[9]
313
314 if (strand_TR =="+") and (start_TR == start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE > end_TR):
315 tmplist.append(line.strip())
316 tmplist.append("gene_in_TE")
317 linelist.append(tmplist)
318 tmplist = []
319
320 # F[1]==================================>F[2]
321 # F[8]----------------------------------------------------------F[9]
322
323 if (strand_TR =="-") and (start_TR == start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE > end_TR):
324 tmplist.append(line.strip())
325 tmplist.append("gene_in_TE")
326 linelist.append(tmplist)
327 tmplist = []
328
329 # F[1]<==================================F[2]
330 # F[8]----------------------------------------------------------F[9]
331
332 favorablecases = "%s_TSSoverlaps_and_TE_closest_TSS_and_inclus_ALL" % bedtoolsfile
333 w = open(favorablecases,'w')
334 for s in linelist:
335 line= "\t".join(str(item) for item in s)
336 w.write("%s\n" % line)
337 w.close()
338
339
340 def getClassCodeCuffcompare(self, tmap_file, bedtools_file):
341 class_code_dic = {}
342 lcode_ref = []
343 tmp = []
344 linetowrite =[]
345 with open(tmap_file) as tmap:
346 tmapline = tmap.readlines()
347 for i in range(1,len(tmapline)):
348 cuff_id = tmapline[i].split("\t")[4].strip()
349 class_code = tmapline[i].split("\t")[2].strip()
350 ref_id = tmapline[i].split("\t")[1].strip()
351 lcode_ref.append(class_code)
352 lcode_ref.append(ref_id)
353 class_code_dic[cuff_id] = lcode_ref
354 lcode_ref = []
355
356 with open(bedtools_file) as bedtools:
357 bedtoolsline = bedtools.readlines()
358 for i in xrange(0,len(bedtoolsline)):
359 tmp = bedtoolsline[i].strip().split("\t")
360 transcript_bedtools = bedtoolsline[i].split("\t")[3].strip()
361 if transcript_bedtools in class_code_dic.keys():
362 tmp.append(class_code_dic[transcript_bedtools][0])
363 tmp.append(class_code_dic[transcript_bedtools][1])
364 else:
365 tmp.append("NA")
366 tmp.append("NA")
367
368 linetowrite.append(tmp)
369 tmp=[]
370
371
372 output = "%s_with_Ref" % bedtools_file
373 w = open(output,'w')
374 line = ""
375 for i in xrange(0,len(linetowrite)):
376 for j in range(0,17):
377 line = line + linetowrite[i][j] + "\t"
378 w.write(line)
379 w.write("\n")
380 line = ""
381 w.close()
382
383 def run(self):
384 self.checkOptions()
385 try:
386 LoggerFactory.setLevel(self._log, self._verbosity)
387 exeDir = os.getcwd()
388 workingDir = "out_TEiso_%s" % time.strftime("%Y%m%d%H%M%S")
389 if os.path.exists(workingDir):
390 self._logAndRaise("ERROR: %s already exists." % workingDir)
391 os.mkdir(workingDir)
392 referencefile = os.path.abspath(self._reference)
393 transcriptsfile = os.path.abspath(self._transcripts)
394 TEfile = os.path.abspath(self._TE)
395 print "workingDir >>>>> ",workingDir
396 os.symlink("%s" % os.path.abspath(self._reference), "%s/%s" % (workingDir, os.path.basename(self._reference)))
397 os.symlink("%s" % os.path.abspath(self._transcripts), "%s/%s" % (workingDir, os.path.basename(self._transcripts)))
398 os.chdir(workingDir)
399 bowtie_build_Dir = "bowtie_build"
400 prefixbowtie = os.path.basename(self._reference).split(".")[0]
401 iLaunchBowtie = Bowtie_build(referencefile, prefixbowtie, bowtie_build_Dir)
402 iLaunchBowtie.run()
403 os.chdir(exeDir)
404 self._log.info("Indexing genome is finished!!!!")
405 tophat_Dir = "tophat"
406 if self._type == "single":
407 l_single_reads = []
408 for reads in range(0, len(self._single_reads)):
409 os.symlink("%s" % os.path.abspath(self._single_reads[reads]), "%s/%s" % (workingDir, os.path.basename(self._single_reads[reads])))
410 filename = os.path.splitext(self._single_reads[reads])[0]
411 filetype = os.path.splitext(self._single_reads[reads])[1]
412 if filetype == ".gz":
413 os.system("gunzip -c %s > %s/%s" % (self._single_reads[reads], workingDir, os.path.basename(filename)))
414 if filetype == ".bz2":
415 os.system("bunzip2 -c %s > %s/%s" % (os.path.abspath(self._single_reads[reads]), workingDir, os.path.basename(filename)))
416 if filetype ==".fq":
417 filename = self._single_reads[reads]
418 l_single_reads.append("%s" % os.path.basename(filename))
419 bowtiePrefix = "%s/%s" % (bowtie_build_Dir, prefixbowtie)
420 path = ("%s/%s") % (exeDir,workingDir)
421 os.chdir(path)
422 iLaunchTophat = Tophat(tophat_Dir, bowtiePrefix, self._type, l_single_reads, self._left_reads, self._right_reads)
423 iLaunchTophat.run()
424 if self._type == "paired":
425 l_left_reads = []
426 l_right_reads = []
427 for reads in range(0, len(self._left_reads)):
428 os.symlink("%s" % os.path.abspath(self._left_reads[reads]), "%s/%s" % (workingDir, os.path.basename(self._left_reads[reads])))
429 filename = os.path.splitext(self._left_reads[reads])[0]
430 filetype = os.path.splitext(self._left_reads[reads])[1]
431 ##TODO : check type input file: mimetypes.guess_type(self._single_reads[reads])
432 if filetype == ".gz":
433 os.system("gunzip -c %s > %s/%s" % (self._left_reads[reads],workingDir, os.path.basename(filename)))
434 if filetype == ".bz2":
435 os.system("bunzip2 -c %s > %s/%s" % (self._left_reads[reads],workingDir, os.path.basename(filename)))
436 if filetype ==".fq":
437 filename = self._left_reads[reads]
438 l_left_reads.append("%s" % os.path.basename(filename))
439
440 for reads in range(0, len(self._right_reads)):
441 os.symlink("%s" % os.path.abspath(self._right_reads[reads]), "%s/%s" % (workingDir, os.path.basename(self._right_reads[reads])))
442 filename = os.path.splitext(self._right_reads[reads])[0]
443 filetype = os.path.splitext(self._right_reads[reads])[1]
444 if filetype == ".gz":
445 os.system("gunzip -c %s > %s/%s" % (self._right_reads[reads],workingDir, os.path.basename(filename)))
446 if filetype == ".bz2":
447 os.system("bunzip2 -c %s > %s/%s" % (self._right_reads[reads],workingDir, os.path.basename(filename)))
448 if filetype ==".fq":
449 filename = self._right_reads[reads]
450 l_right_reads.append("%s" % os.path.basename(filename))
451 bowtiePrefix = "%s/%s" % (bowtie_build_Dir, prefixbowtie)
452 path= ("%s/%s") % (exeDir,workingDir)
453 os.chdir(path)
454 iLaunchTophat = Tophat(tophat_Dir, bowtiePrefix, self._type, self._single_reads, l_left_reads, l_right_reads)
455 iLaunchTophat.run()
456 self._log.info("Mapping reads is finished!!!!")
457
458 if self._assembly_tool == "cufflinks":
459 cufflinks_Dir = "cufflinks"
460 accepted_hits = "%s/accepted_hits.bam" % tophat_Dir
461 iLaunchCufflinks = Cufflinks(accepted_hits, transcriptsfile , cufflinks_Dir)
462 iLaunchCufflinks.run()
463 self._log.info("%s is finished!!!!" % self._assembly_tool)
464 os.symlink("cufflinks/transcripts.gtf", "transcripts.gtf")
465 cuffcompare_Dir = "cuffcompare"
466 transcripts = "transcripts.gtf"
467 iLaunchCuffcompare = Cuffcompare(transcriptsfile, transcripts, outprefix = "cuffcompare", workingDir = cuffcompare_Dir)
468 iLaunchCuffcompare.run()
469 self._log.info("Cuffcompare is finished!!!!")
470
471
472 bedtools_closest_Dir = "bedtools_closest"
473 os.mkdir(bedtools_closest_Dir)
474 os.chdir(bedtools_closest_Dir)
475
476 transcriptsgtf = "%s_transcripts.gtf" % self._assembly_tool
477 os.symlink("../%s/transcripts.gtf" % self._assembly_tool,transcriptsgtf)
478 transcriptsbed = "%s_transcripts.bed" % self._assembly_tool
479 self.getTranscriptToBed(transcriptsgtf,transcriptsbed)
480 TEgff = os.path.basename(os.path.splitext(TEfile)[0]) + ".gff3"
481 TEbed = os.path.basename(os.path.splitext(TEfile)[0]) + ".bed"
482 os.symlink("%s" % TEfile,TEgff)
483 self.getTEGFFToBed(TEgff,TEbed)
484 iLauncherBdc= Bedtools_closest(transcriptsbed, TEbed, "bedtools_closest_%s" % transcriptsgtf.split(".")[0])
485 iLauncherBdc.run()
486 self._log.info("Bedtools closest is finished!!!!")
487 bedtoolsfile = "bedtools_closest_%s" % transcriptsgtf.split(".")[0]
488 self.getTEnearPromoter(bedtoolsfile)
489 tmap_file = "../cuffcompare/cuffcompare.transcripts.gtf.tmap"
490 bedtools_file = "%s_TSSoverlaps_and_TE_closest_TSS_and_inclus_ALL" % bedtoolsfile
491
492 self.getClassCodeCuffcompare(tmap_file,bedtools_file)
493 os.chdir("..")
494 self._log.info("Done!!!!")
495
496 except Exception:
497 self._logAndRaise("ERROR in TEiso")
498
499
500 if __name__ == "__main__":
501 iLaunch = LaunchTEiso()
502 iLaunch._setAttributesFromCmdLine()
503 iLaunch.run()