6
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """
+ − 32 Read a mapping file (many formats supported) and select some of them
+ − 33 Mappings should be sorted by read names
+ − 34 """
+ − 35 import os, random, shelve
+ − 36 from optparse import OptionParser, OptionGroup
+ − 37 from commons.core.parsing.ParserChooser import ParserChooser
+ − 38 from commons.core.parsing.FastaParser import FastaParser
+ − 39 from commons.core.parsing.FastqParser import FastqParser
+ − 40 from commons.core.parsing.GffParser import GffParser
+ − 41 from commons.core.writer.BedWriter import BedWriter
+ − 42 from commons.core.writer.UcscWriter import UcscWriter
+ − 43 from commons.core.writer.GbWriter import GbWriter
+ − 44 from commons.core.writer.Gff2Writer import Gff2Writer
+ − 45 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 46 from commons.core.writer.FastaWriter import FastaWriter
+ − 47 from commons.core.writer.FastqWriter import FastqWriter
+ − 48 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+ − 49 from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection
+ − 50 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
+ − 51 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 52 from SMART.Java.Python.misc.Progress import Progress
+ − 53 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 54
+ − 55
+ − 56 distanceExons = 20
+ − 57 exonSize = 20
+ − 58
+ − 59
+ − 60 class MapperAnalyzer(object):
+ − 61 """
+ − 62 Analyse the output of a parser
+ − 63 """
+ − 64
+ − 65 def __init__(self, verbosity = 0):
+ − 66 self.verbosity = verbosity
+ − 67 self.mySqlConnection = MySqlConnection(verbosity)
+ − 68 self.tooShort = 0
+ − 69 self.tooManyMismatches = 0
+ − 70 self.tooManyGaps = 0
+ − 71 self.tooShortExons = 0
+ − 72 self.tooManyMappings = 0
+ − 73 self.nbMappings = 0
+ − 74 self.nbSequences = 0
+ − 75 self.nbAlreadyMapped = 0
+ − 76 self.nbAlreadyMappedSequences = 0
+ − 77 self.nbWrittenMappings = 0
+ − 78 self.nbWrittenSequences = 0
+ − 79 self.parser = None
+ − 80 self.logHandle = None
+ − 81 self.randomNumber = random.randint(0, 100000)
+ − 82 self.gff3Writer = None
+ − 83 self.alreadyMappedReader = None
+ − 84 self.unmatchedWriter = None
+ − 85 self.sequenceListParser = None
+ − 86 self.sequences = None
+ − 87 self.alreadyMapped = None
+ − 88 self.mappedNamesTable = None
+ − 89 self.minSize = None
+ − 90 self.minId = None
+ − 91 self.maxMismatches = None
+ − 92 self.maxGaps = None
+ − 93 self.maxMappings = None
+ − 94 self.merge = False
+ − 95 self.checkExons = False
+ − 96 self.suffix = None
+ − 97 self.tmpDirectory = "%s%s" % (os.environ["SMARTMPPATH"], os.sep) if "SMARTMPPATH" in os.environ else ""
+ − 98
+ − 99
+ − 100 def __del__(self):
+ − 101 if self.sequences != None:
+ − 102 self.sequences.close()
+ − 103 if self.alreadyMapped != None:
+ − 104 self.alreadyMapped.close()
+ − 105 if self.mappedNamesTable != None:
+ − 106 self.mappedNamesTable.remove()
+ − 107 if self.gff3Writer != None:
+ − 108 self.gff3Writer.close()
+ − 109
+ − 110 if self.logHandle != None:
+ − 111 self.logHandle.close()
+ − 112
+ − 113
+ − 114 def setMappingFile(self, fileName, format):
+ − 115 parserChooser = ParserChooser(self.verbosity)
+ − 116 parserChooser.findFormat(format, "mapping")
+ − 117 self.parser = parserChooser.getParser(fileName)
+ − 118
+ − 119
+ − 120 def setSequenceFile(self, fileName, format):
+ − 121 if format == "fasta":
+ − 122 self.sequenceListParser = FastaParser(fileName, self.verbosity)
+ − 123 elif format == "fastq":
+ − 124 self.sequenceListParser = FastqParser(fileName, self.verbosity)
+ − 125 else:
+ − 126 raise Exception("Do not understand sequence format %s" % (format))
+ − 127
+ − 128
+ − 129 def setOutputFile(self, fileName, title):
+ − 130 self.gff3Writer = Gff3Writer(fileName, self.verbosity)
+ − 131 self.gff3Writer.setTitle(title)
+ − 132
+ − 133
+ − 134 def setAlreadyMatched(self, fileName):
+ − 135 self.alreadyMappedReader = GffParser(fileName, self.verbosity)
+ − 136
+ − 137
+ − 138 def setRemainingFile(self, fileName, format):
+ − 139 if format == "fasta":
+ − 140 self.unmatchedWriter = FastaWriter("%s_unmatched.fasta" % (fileName), self.verbosity)
+ − 141 elif format == "fastq":
+ − 142 self.unmatchedWriter = FastqWriter("%s_unmatched.fastq" % (fileName), self.verbosity)
+ − 143 else:
+ − 144 raise Exception("Do not understand %s format." % (format))
+ − 145 self.mappedNamesTable = MySqlTable(self.mySqlConnection, "mappedNames_%d" % (self.randomNumber), self.verbosity)
+ − 146 self.mappedNamesTable.create(["name"], {"name": "char"}, {"name": 50})
+ − 147 self.mappedNamesTable.createIndex("iNameMapped", ["name", ], True)
+ − 148
+ − 149
+ − 150 def setLog(self, fileName):
+ − 151 self.logHandle = open(fileName, "w")
+ − 152
+ − 153
+ − 154 def setMinSize(self, size):
+ − 155 self.minSize = size
+ − 156
+ − 157
+ − 158 def setMinId(self, id):
+ − 159 self.minId = id
+ − 160
+ − 161
+ − 162 def setMaxMismatches(self, mismatches):
+ − 163 self.maxMismatches = mismatches
+ − 164
+ − 165
+ − 166 def setMaxGaps(self, gaps):
+ − 167 self.maxGaps = gaps
+ − 168
+ − 169
+ − 170 def setMaxMappings(self, mappings):
+ − 171 self.maxMappings = mappings
+ − 172
+ − 173
+ − 174 def mergeExons(self, b):
+ − 175 self.merge = b
+ − 176
+ − 177
+ − 178 def acceptShortExons(self, b):
+ − 179 self.checkExons = not b
+ − 180
+ − 181
+ − 182 def countMappings(self):
+ − 183 self.nbMappings = self.parser.getNbMappings()
+ − 184 if self.verbosity > 0:
+ − 185 print "%i matches found" % (self.nbMappings)
+ − 186
+ − 187
+ − 188 def storeAlreadyMapped(self):
+ − 189 self.alreadyMapped = shelve.open("%stmpAlreadyMapped_%d" % (self.tmpDirectory, self.randomNumber))
+ − 190 progress = Progress(self.alreadyMappedReader.getNbTranscripts(), "Reading already mapped reads", self.verbosity)
+ − 191 self.nbAlreadyMappedSequences = 0
+ − 192 for transcript in self.alreadyMappedReader.getIterator():
+ − 193 if not self.alreadyMapped.has_key(transcript.getName()):
+ − 194 self.alreadyMapped[transcript.getName()] = 1
+ − 195 self.nbAlreadyMappedSequences += 1
+ − 196 progress.inc()
+ − 197 progress.done()
+ − 198 self.nbAlreadyMapped = self.alreadyMappedReader.getNbTranscripts()
+ − 199
+ − 200
+ − 201 def storeSequences(self):
+ − 202 self.sequences = shelve.open("%stmpSequences_%d" % (self.tmpDirectory, self.randomNumber))
+ − 203 progress = Progress(self.sequenceListParser.getNbSequences(), "Reading sequences", self.verbosity)
+ − 204 for sequence in self.sequenceListParser.getIterator():
+ − 205 self.sequences[sequence.getName().split(" ")[0]] = len(sequence.getSequence())
+ − 206 self.nbSequences += 1
+ − 207 progress.inc()
+ − 208 progress.done()
+ − 209 if self.verbosity > 0:
+ − 210 print "%i sequences read" % (self.nbSequences)
+ − 211
+ − 212
+ − 213 def checkOrder(self):
+ − 214 names = shelve.open("%stmpNames_%d" % (self.tmpDirectory, self.randomNumber))
+ − 215 previousName = None
+ − 216 progress = Progress(self.nbMappings, "Checking mapping file", self.verbosity)
+ − 217 for mapping in self.parser.getIterator():
+ − 218 name = mapping.queryInterval.getName()
+ − 219 if name != previousName and previousName != None:
+ − 220 if names.has_key(previousName):
+ − 221 raise Exception("Error! Input mapping file is not ordered! (Name '%s' occurs at least twice)" % (previousName))
+ − 222 names[previousName] = 1
+ − 223 previousName = name
+ − 224 progress.inc()
+ − 225 progress.done()
+ − 226 names.close()
+ − 227
+ − 228
+ − 229 def checkPreviouslyMapped(self, name):
+ − 230 if self.alreadyMappedReader == None:
+ − 231 return False
+ − 232 return self.alreadyMapped.has_key(name)
+ − 233
+ − 234
+ − 235 def findOriginalSize(self, name):
+ − 236 alternate = "%s/1" % (name)
+ − 237 if (self.suffix == None) or (not self.suffix):
+ − 238 if self.sequences.has_key(name):
+ − 239 self.suffix = False
+ − 240 return self.sequences[name]
+ − 241 if self.suffix == None:
+ − 242 self.suffix = True
+ − 243 else:
+ − 244 raise Exception("Cannot find name %n" % (name))
+ − 245 if (self.suffix):
+ − 246 if self.sequences.has_key(alternate):
+ − 247 return self.sequences[alternate]
+ − 248 raise Exception("Cannot find name %s" % (name))
+ − 249
+ − 250
+ − 251 def checkErrors(self, mapping):
+ − 252 accepted = True
+ − 253 # short size
+ − 254 if self.minSize != None and mapping.size * 100 < self.minSize * mapping.queryInterval.size:
+ − 255 self.tooShort += 1
+ − 256 accepted = False
+ − 257 if self.logHandle != None:
+ − 258 self.logHandle.write("size of mapping %s is too short (%i instead of %i)\n" % (str(mapping), mapping.queryInterval.size, mapping.size))
+ − 259 # low identity
+ − 260 if self.minId != None and mapping.getTagValue("identity") < self.minId:
+ − 261 self.tooManyMismatches += 1
+ − 262 accepted = False
+ − 263 if self.logHandle != None:
+ − 264 self.logHandle.write("mapping %s has a low identity rate\n" % (str(mapping)))
+ − 265 # too many mismatches
+ − 266 if self.maxMismatches != None and mapping.getTagValue("nbMismatches") > self.maxMismatches:
+ − 267 self.tooManyMismatches += 1
+ − 268 accepted = False
+ − 269 if self.logHandle != None:
+ − 270 self.logHandle.write("mapping %s has more mismatches than %i\n" % (str(mapping), self.maxMismatches))
+ − 271 # too many gaps
+ − 272 if self.maxGaps != None and mapping.getTagValue("nbGaps") > self.maxGaps:
+ − 273 self.tooManyGaps += 1
+ − 274 accepted = False
+ − 275 if self.logHandle != None:
+ − 276 self.logHandle.write("mapping %s has more gaps than %i\n" % (str(mapping), self.maxGaps))
+ − 277 # short exons
+ − 278 if self.checkExons and len(mapping.subMappings) > 1 and min([subMapping.targetInterval.getSize() for subMapping in mapping.subMappings]) < exonSize:
+ − 279 self.tooShortExons += 1
+ − 280 accepted = False
+ − 281 if self.logHandle != None:
+ − 282 self.logHandle.write("sequence %s maps as too short exons\n" % (mapping))
+ − 283 return accepted
+ − 284
+ − 285
+ − 286 def checkNbMappings(self, mappings):
+ − 287 nbOccurrences = 0
+ − 288 for mapping in mappings:
+ − 289 nbOccurrences += 1 if "nbOccurrences" not in mapping.getTagNames() else mapping.getTagValue("nbOccurrences")
+ − 290 if (self.maxMappings != None and nbOccurrences > self.maxMappings):
+ − 291 self.tooManyMappings += 1
+ − 292 if self.logHandle != None:
+ − 293 self.logHandle.write("sequence %s maps %i times\n" % (mappings[0].queryInterval.getName(), nbOccurrences))
+ − 294 return False
+ − 295 return (nbOccurrences > 0)
+ − 296
+ − 297
+ − 298 def sortMappings(self, mappings):
+ − 299 nbOccurrences = 0
+ − 300 for mapping in mappings:
+ − 301 nbOccurrences += 1 if "nbOccurrences" not in mapping.getTagNames() else mapping.getTagValue("nbOccurrences")
+ − 302
+ − 303 orderedMappings = sorted(mappings, key = lambda mapping: mapping.getErrorScore())
+ − 304 cpt = 1
+ − 305 rank = 1
+ − 306 previousMapping = None
+ − 307 previousScore = None
+ − 308 wasLastTie = False
+ − 309 rankedMappings = []
+ − 310 bestRegion = "%s:%d-%d" % (orderedMappings[0].targetInterval.getChromosome(), orderedMappings[0].targetInterval.getStart(), orderedMappings[0].targetInterval.getEnd())
+ − 311 for mapping in orderedMappings:
+ − 312 mapping.setNbOccurrences(nbOccurrences)
+ − 313 mapping.setOccurrence(cpt)
+ − 314
+ − 315 score = mapping.getErrorScore()
+ − 316 if previousScore != None and previousScore == score:
+ − 317 if "Rank" in previousMapping.getTagNames():
+ − 318 if not wasLastTie:
+ − 319 previousMapping.setRank("%sTie" % (rank))
+ − 320 mapping.setRank("%sTie" % (rank))
+ − 321 wasLastTie = True
+ − 322 else:
+ − 323 rank = cpt
+ − 324 mapping.setRank(rank)
+ − 325 wasLastTie = False
+ − 326 if cpt != 1:
+ − 327 mapping.setBestRegion(bestRegion)
+ − 328
+ − 329 rankedMappings.append(mapping)
+ − 330 previousMapping = mapping
+ − 331 previousScore = score
+ − 332 cpt += 1
+ − 333 return rankedMappings
+ − 334
+ − 335
+ − 336 def processMappings(self, mappings):
+ − 337 if not mappings:
+ − 338 return
+ − 339 selectedMappings = []
+ − 340 name = mappings[0].queryInterval.getName()
+ − 341 size = self.findOriginalSize(name)
+ − 342 for mapping in mappings:
+ − 343 if self.merge:
+ − 344 mapping.mergeExons(distanceExons)
+ − 345 mapping.queryInterval.size = size
+ − 346 if self.checkErrors(mapping):
+ − 347 selectedMappings.append(mapping)
+ − 348
+ − 349 if self.checkNbMappings(selectedMappings):
+ − 350 if self.unmatchedWriter != None:
+ − 351 query = self.mySqlConnection.executeQuery("INSERT INTO %s (name) VALUES ('%s')" % (self.mappedNamesTable.name, name if not self.suffix else "%s/1" % (name)))
+ − 352 self.nbWrittenSequences += 1
+ − 353 mappings = self.sortMappings(selectedMappings)
+ − 354 for mapping in mappings:
+ − 355 self.nbWrittenMappings += 1
+ − 356 self.gff3Writer.addTranscript(mapping.getTranscript())
+ − 357
+ − 358
+ − 359 def readMappings(self):
+ − 360 previousQueryName = None
+ − 361 mappings = []
+ − 362 self.parser.reset()
+ − 363 progress = Progress(self.nbMappings, "Reading mappings", self.verbosity)
+ − 364 for mapping in self.parser.getIterator():
+ − 365 queryName = mapping.queryInterval.getName().split(" ")[0]
+ − 366 if self.checkPreviouslyMapped(queryName):
+ − 367 if self.logHandle != None:
+ − 368 self.logHandle.write("Mapping %s has already been mapped.\n" % (queryName))
+ − 369 else:
+ − 370 if previousQueryName == queryName:
+ − 371 mappings.append(mapping)
+ − 372 else:
+ − 373 if previousQueryName != None:
+ − 374 self.processMappings(mappings)
+ − 375 previousQueryName = queryName
+ − 376 mappings = [mapping, ]
+ − 377 progress.inc()
+ − 378 self.processMappings(mappings)
+ − 379 self.gff3Writer.write()
+ − 380 self.gff3Writer.close()
+ − 381 progress.done()
+ − 382
+ − 383
+ − 384 def writeUnmatched(self):
+ − 385 progress = Progress(self.nbSequences, "Reading unmatched sequences", self.verbosity)
+ − 386 for sequence in self.sequenceListParser.getIterator():
+ − 387 name = sequence.getName().split(" ")[0]
+ − 388 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE name = '%s' LIMIT 1" % (self.mappedNamesTable.name, name))
+ − 389 if query.isEmpty():
+ − 390 self.unmatchedWriter.addSequence(sequence)
+ − 391 progress.inc()
+ − 392 progress.done()
+ − 393
+ − 394
+ − 395 def analyze(self):
+ − 396 self.countMappings()
+ − 397 self.checkOrder()
+ − 398 self.storeSequences()
+ − 399 if self.alreadyMappedReader != None:
+ − 400 self.storeAlreadyMapped()
+ − 401 self.readMappings()
+ − 402 if self.unmatchedWriter != None:
+ − 403 self.writeUnmatched()
+ − 404
+ − 405
+ − 406
+ − 407
+ − 408 if __name__ == "__main__":
+ − 409
+ − 410 # parse command line
+ − 411 description = "Mapper Analyzer v1.0.1: Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. [Category: Conversion]"
+ − 412
+ − 413 parser = OptionParser(description = description)
+ − 414 compGroup = OptionGroup(parser, "Compulsory options")
+ − 415 filtGroup = OptionGroup(parser, "Filtering options")
+ − 416 tranGroup = OptionGroup(parser, "Transformation options")
+ − 417 outpGroup = OptionGroup(parser, "Output options")
+ − 418 otheGroup = OptionGroup(parser, "Other options")
+ − 419 compGroup.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file (output of the tool) [compulsory] [format: file in mapping format given by -f]")
+ − 420 compGroup.add_option("-f", "--format", dest="format", action="store", default="seqmap", type="string", help="format of the file [compulsory] [format: mapping file format]")
+ − 421 compGroup.add_option("-q", "--sequences", dest="sequencesFileName", action="store", type="string", help="file of the sequences [compulsory] [format: file in sequence format given by -k]")
+ − 422 compGroup.add_option("-k", "--seqFormat", dest="sequenceFormat", action="store", default="fasta", type="string", help="format of the sequences: fasta or fastq [default: fasta] [format: sequence file format]")
+ − 423 compGroup.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 424 filtGroup.add_option("-n", "--number", dest="number", action="store", default=None, type="int", help="max. number of occurrences of a sequence [format: int]")
+ − 425 filtGroup.add_option("-s", "--size", dest="size", action="store", default=None, type="int", help="minimum pourcentage of size [format: int]")
+ − 426 filtGroup.add_option("-d", "--identity", dest="identity", action="store", default=None, type="int", help="minimum pourcentage of identity [format: int]")
+ − 427 filtGroup.add_option("-m", "--mismatch", dest="mismatch", action="store", default=None, type="int", help="maximum number of mismatches [format: int]")
+ − 428 filtGroup.add_option("-p", "--gap", dest="gap", action="store", default=None, type="int", help="maximum number of gaps [format: int]")
+ − 429 tranGroup.add_option("-e", "--mergeExons", dest="mergeExons", action="store_true", default=False, help="merge exons when introns are short [format: bool] [default: false]")
+ − 430 tranGroup.add_option("-x", "--removeExons", dest="removeExons", action="store_true", default=False, help="remove transcripts when exons are short [format: bool] [default: false]")
+ − 431 outpGroup.add_option("-t", "--title", dest="title", action="store", default="SMART", type="string", help="title of the UCSC track [format: string] [default: SMART]")
+ − 432 outpGroup.add_option("-r", "--remaining", dest="remaining", action="store_true", default=False, help="print the unmatched sequences [format: bool] [default: false]")
+ − 433 otheGroup.add_option("-a", "--append", dest="appendFileName", action="store", default=None, type="string", help="append to GFF3 file [format: file in GFF3 format]")
+ − 434 otheGroup.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
+ − 435 otheGroup.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 436 parser.add_option_group(compGroup)
+ − 437 parser.add_option_group(filtGroup)
+ − 438 parser.add_option_group(tranGroup)
+ − 439 parser.add_option_group(outpGroup)
+ − 440 parser.add_option_group(otheGroup)
+ − 441 (options, args) = parser.parse_args()
+ − 442
+ − 443
+ − 444 analyzer = MapperAnalyzer(options.verbosity)
+ − 445 analyzer.setMappingFile(options.inputFileName, options.format)
+ − 446 analyzer.setSequenceFile(options.sequencesFileName, options.sequenceFormat)
+ − 447 analyzer.setOutputFile(options.outputFileName, options.title)
+ − 448 if options.appendFileName != None:
+ − 449 analyzer.setAlreadyMatched(options.appendFileName)
+ − 450 if options.remaining:
+ − 451 analyzer.setRemainingFile(options.outputFileName, options.sequenceFormat)
+ − 452 if options.number != None:
+ − 453 analyzer.setMaxMappings(options.number)
+ − 454 if options.size != None:
+ − 455 analyzer.setMinSize(options.size)
+ − 456 if options.identity != None:
+ − 457 analyzer.setMinId(options.identity)
+ − 458 if options.mismatch != None:
+ − 459 analyzer.setMaxMismatches(options.mismatch)
+ − 460 if options.gap != None:
+ − 461 analyzer.setMaxGaps(options.gap)
+ − 462 if options.mergeExons:
+ − 463 analyzer.mergeExons(True)
+ − 464 if options.removeExons:
+ − 465 analyzer.acceptShortExons(False)
+ − 466 if options.log:
+ − 467 analyzer.setLog("%s.log" % (options.outputFileName))
+ − 468 analyzer.analyze()
+ − 469
+ − 470 if options.verbosity > 0:
+ − 471 print "kept %i sequences over %s (%f%%)" % (analyzer.nbWrittenSequences, analyzer.nbSequences, float(analyzer.nbWrittenSequences) / analyzer.nbSequences * 100)
+ − 472 if options.appendFileName != None:
+ − 473 print "kept %i sequences over %s (%f%%) including already mapped sequences" % (analyzer.nbWrittenSequences + analyzer.nbAlreadyMappedSequences, analyzer.nbSequences, float(analyzer.nbWrittenSequences + analyzer.nbAlreadyMappedSequences) / analyzer.nbSequences * 100)
+ − 474 print "kept %i mappings over %i (%f%%)" % (analyzer.nbWrittenMappings, analyzer.nbMappings, float(analyzer.nbWrittenMappings) / analyzer.nbMappings * 100)
+ − 475 if options.appendFileName != None:
+ − 476 print "kept %i mappings over %i (%f%%) including already mapped" % (analyzer.nbWrittenMappings + analyzer.nbAlreadyMapped, analyzer.nbMappings, float(analyzer.nbWrittenMappings + analyzer.nbAlreadyMapped) / analyzer.nbMappings * 100)
+ − 477 print "removed %i too short mappings (%f%%)" % (analyzer.tooShort, float(analyzer.tooShort) / analyzer.nbMappings * 100)
+ − 478 print "removed %i mappings with too many mismatches (%f%%)" % (analyzer.tooManyMismatches, float(analyzer.tooManyMismatches) / analyzer.nbMappings * 100)
+ − 479 print "removed %i mappings with too many gaps (%f%%)" % (analyzer.tooManyGaps, float(analyzer.tooManyGaps) / analyzer.nbMappings * 100)
+ − 480 print "removed %i mappings with too short exons (%f%%)" % (analyzer.tooShortExons, float(analyzer.tooShortExons) / analyzer.nbMappings * 100)
+ − 481 print "removed %i sequences with too many hits (%f%%)" % (analyzer.tooManyMappings, float(analyzer.tooManyMappings) / analyzer.nbSequences * 100)
+ − 482 print "%i sequences have no mapping (%f%%)" % (analyzer.nbSequences - analyzer.nbWrittenSequences, float(analyzer.nbSequences - analyzer.nbWrittenSequences) / analyzer.nbSequences * 100)
+ − 483 if options.appendFileName != None:
+ − 484 print "%i sequences have no mapping (%f%%) excluding already mapped sequences" % (analyzer.nbSequences - analyzer.nbWrittenSequences - analyzer.nbAlreadyMappedSequences, float(analyzer.nbSequences - analyzer.nbWrittenSequences - analyzer.nbAlreadyMappedSequences) / analyzer.nbSequences * 100)
+ − 485
+ − 486
