Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/BowtieParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2011 |
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3 # |
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4 # This software is governed by the CeCILL license under French law and |
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5 # abiding by the rules of distribution of free software. You can use, |
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6 # modify and/ or redistribute the software under the terms of the CeCILL |
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7 # license as circulated by CEA, CNRS and INRIA at the following URL |
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8 # "http://www.cecill.info". |
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9 # |
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10 # As a counterpart to the access to the source code and rights to copy, |
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11 # modify and redistribute granted by the license, users are provided only |
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12 # with a limited warranty and the software's author, the holder of the |
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13 # economic rights, and the successive licensors have only limited |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability. |
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15 # |
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16 # In this respect, the user's attention is drawn to the risks associated |
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17 # with loading, using, modifying and/or developing or reproducing the |
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18 # software by the user in light of its specific status of free software, |
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19 # that may mean that it is complicated to manipulate, and that also |
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20 # therefore means that it is reserved for developers and experienced |
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21 # professionals having in-depth computer knowledge. Users are therefore |
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22 # encouraged to load and test the software's suitability as regards their |
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23 # requirements in conditions enabling the security of their systems and/or |
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24 # data to be ensured and, more generally, to use and operate it in the |
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25 # same conditions as regards security. |
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26 # |
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27 # The fact that you are presently reading this means that you have had |
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28 # knowledge of the CeCILL license and that you accept its terms. |
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29 # |
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30 import re |
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31 import sys |
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32 from commons.core.parsing.MapperParser import MapperParser |
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33 from SMART.Java.Python.structure.Mapping import Mapping |
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34 from SMART.Java.Python.structure.SubMapping import SubMapping |
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35 from SMART.Java.Python.structure.Interval import Interval |
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36 |
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37 class BowtieParser(MapperParser): |
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38 """A class that parses BowTie format""" |
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39 |
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40 def __init__(self, fileName, verbosity = 0): |
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41 super(BowtieParser, self).__init__(fileName, verbosity) |
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42 |
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43 |
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44 def __del__(self): |
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45 super(BowtieParser, self).__del__() |
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46 |
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47 |
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48 def getFileFormats(): |
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49 return ["bowtie"] |
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50 getFileFormats = staticmethod(getFileFormats) |
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51 |
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52 |
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53 def skipFirstLines(self): |
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54 pass |
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55 |
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56 |
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57 def parseLine(self, line): |
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58 line = line.strip() |
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59 fields = line.split("\t") |
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60 if len(fields) not in (7, 8): |
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61 raise Exception("Line %d '%s' does not look like a BowTie line (number of fields is %d instead of 7 or 8)" % (self.currentLineNb, line, len(fields))) |
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62 name = fields[0] |
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63 direction = 1 if fields[1] == "+" else -1 |
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64 chromosome = fields[2] |
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65 genomeStart = int(fields[3]) + 1 |
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66 sequence = fields[4] |
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67 quality = fields[5] |
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68 number = int(fields[6]) |
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69 nbMismatches = 0 |
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70 if len(fields) == 8: |
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71 tags = fields[7] |
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72 nbMismatches = len(tags.split(",")) |
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73 |
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74 mapping = Mapping() |
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75 queryInterval = Interval() |
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76 queryInterval.setName(name) |
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77 queryInterval.setStart(1) |
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78 queryInterval.setEnd(len(sequence) + 1) |
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79 targetInterval = Interval() |
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80 targetInterval.setChromosome(chromosome) |
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81 targetInterval.setStart(genomeStart) |
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82 targetInterval.setEnd(genomeStart + len(sequence) - 1) |
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83 subMapping = SubMapping() |
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84 subMapping.setQueryInterval(queryInterval) |
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85 subMapping.setTargetInterval(targetInterval) |
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86 mapping.addSubMapping(subMapping) |
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87 mapping.setSize(len(sequence)) |
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88 mapping.setNbMismatches(nbMismatches) |
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89 mapping.setDirection(direction) |
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90 return mapping |
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91 |