Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/SamParser.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # import re import sys from commons.core.parsing.MapperParser import MapperParser from SMART.Java.Python.structure.Mapping import Mapping from SMART.Java.Python.structure.SubMapping import SubMapping from SMART.Java.Python.structure.Interval import Interval class SamParser(MapperParser): """A class that parses SAM format (as given by BWA)""" def __init__(self, fileName, verbosity = 0): super(SamParser, self).__init__(fileName, verbosity) def __del__(self): super(SamParser, self).__del__() def getFileFormats(): return ["sam"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def getInfos(self): self.chromosomes = set() self.nbMappings = 0 self.size = 0 self.reset() if self.verbosity >= 10: print "Getting information on SAM file" self.reset() for line in self.handle: line = line.strip() if line == "" or line[0] == "@": continue parts = line.split("\t") chromosome = parts[2] if chromosome != "*": self.chromosomes.add(chromosome) self.nbMappings += 1 self.size += len(parts[8]) if self.verbosity >= 10 and self.nbMappings % 100000 == 0: sys.stdout.write(" %d mappings read\r" % (self.nbMappings)) sys.stdout.flush() self.reset() if self.verbosity >= 10: print " %d mappings read" % (self.nbMappings) print "Done." def parseLine(self, line): line = line.strip() if line[0] == "@": return fields = line.split("\t") if len(fields) < 11: raise Exception("Line %d '%s' does not look like a SAM line (number of fields is %d instead of 11)" % (self.currentLineNb, line, len(fields))) name = fields[0] flag = int(fields[1]) if (flag & 0x4) == 0x4: return None direction = 1 if (flag & 0x10) == 0x0 else -1 chromosome = fields[2] genomeStart = int(fields[3]) quality = fields[4] cigar = fields[5] mate = fields[6] mateGenomeStart = fields[7] gapSize = fields[8] sequence = fields[9] quality = fields[10] tags = fields[11:] if mateGenomeStart != "*": mateGenomeStart = int(mateGenomeStart) mapping = Mapping() nbOccurrences = 1 nbMismatches = 0 nbMatches = 0 nbGaps = 0 subMapping = None queryOffset = 0 targetOffset = 0 currentNumber = 0 readStart = None for tag in tags: key = tag[:2] if key == "X0": nbOccurrences = int(tag[5:]) elif key == "X1": nbOccurrences += int(tag[5:]) elif key == "XM": nbMismatches = int(tag[5:]) mapping.setTagValue("nbOccurrences", nbOccurrences) mapping.setTagValue("quality", int(fields[4])) for char in cigar: m = re.match(r"[0-9]", char) if m != None: currentNumber = currentNumber * 10 + (ord(char) - ord("0")) continue # match m = re.match(r"[M]", char) if m != None: if readStart == None: readStart = queryOffset if subMapping == None: subMapping = SubMapping() subMapping.setSize(currentNumber) subMapping.setDirection(direction) subMapping.queryInterval.setName(name) subMapping.queryInterval.setStart(queryOffset) subMapping.queryInterval.setDirection(direction) subMapping.targetInterval.setChromosome(chromosome) subMapping.targetInterval.setStart(genomeStart + targetOffset) subMapping.targetInterval.setDirection(1) nbMatches += currentNumber targetOffset += currentNumber queryOffset += currentNumber currentNumber = 0 continue # insertion on the read m = re.match(r"[I]", char) if m != None: nbGaps += 1 queryOffset += currentNumber currentNumber = 0 continue # insertion on the genome m = re.match(r"[D]", char) if m != None: if subMapping != None: subMapping.queryInterval.setEnd(queryOffset - 1) subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1) mapping.addSubMapping(subMapping) subMapping = None nbGaps += 1 targetOffset += currentNumber currentNumber = 0 continue # intron m = re.match(r"[N]", char) if m != None: if subMapping != None: subMapping.queryInterval.setEnd(queryOffset - 1) subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1) mapping.addSubMapping(subMapping) subMapping = None targetOffset += currentNumber currentNumber = 0 continue # soft clipping (substitution) m = re.match(r"[S]", char) if m != None: nbMismatches += currentNumber targetOffset += currentNumber queryOffset += currentNumber currentNumber = 0 continue # hard clipping m = re.match(r"[H]", char) if m != None: targetOffset += currentNumber queryOffset += currentNumber currentNumber = 0 continue # padding m = re.match(r"[P]", char) if m != None: continue raise Exception("Do not understand paramer '%s' in line %s" % (char, line)) if subMapping != None: subMapping.queryInterval.setEnd(queryOffset - 1) subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1) mapping.addSubMapping(subMapping) mapping.queryInterval.setStart(readStart) mapping.queryInterval.setEnd(queryOffset - 1) mapping.targetInterval.setEnd(genomeStart + targetOffset - 1) mapping.setNbMismatches(nbMismatches) mapping.setNbGaps(nbGaps) mapping.queryInterval.setName(name) mapping.queryInterval.setDirection(direction) mapping.targetInterval.setChromosome(chromosome) mapping.targetInterval.setStart(genomeStart) mapping.targetInterval.setDirection(direction) mapping.setSize(len(sequence)) mapping.setDirection(direction) return mapping