Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/commons/core/parsing/SamParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/commons/core/parsing/SamParser.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,234 @@ +# +# 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 + +