Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/ShrimpParser.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 2009-2010 |
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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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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 SMART.Java.Python.structure.Mapping import Mapping |
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33 from commons.core.parsing.MapperParser import MapperParser |
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34 |
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35 |
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36 class ShrimpParser(MapperParser): |
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37 """A class that parses the output of Shrimp""" |
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38 |
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39 def __init__(self, fileName, verbosity = 0): |
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40 super(ShrimpParser, self).__init__(fileName, verbosity) |
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41 |
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42 |
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43 def __del__(self): |
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44 super(ShrimpParser, self).__del__() |
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45 |
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46 |
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47 def getFileFormats(): |
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48 return ["shrimp"] |
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49 getFileFormats = staticmethod(getFileFormats) |
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50 |
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51 |
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52 def skipFirstLines(self): |
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53 self.handle.readline() |
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54 self.currentLineNb += 1 |
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55 |
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56 |
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57 def parseLine(self, line): |
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58 m = re.search(r"^\s*>([^\t]+)\t+(\S+)\s+([+-])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*$", line) |
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59 if m == None: |
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60 sys.exit("\nLine %d '%s' does not have a Shrimp format" % (self.currentLineNb, line)) |
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61 |
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62 mapping = Mapping() |
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63 |
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64 mapping.queryInterval.setName(m.group(1)) |
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65 mapping.queryInterval.setStart(min(int(m.group(6)), int(m.group(7)))) |
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66 mapping.queryInterval.setEnd(max(int(m.group(6)), int(m.group(7)))) |
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67 |
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68 mapping.targetInterval.setChromosome(m.group(2)) |
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69 mapping.targetInterval.setStart(min(int(m.group(4)), int(m.group(5)))) |
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70 mapping.targetInterval.setEnd(max(int(m.group(4)), int(m.group(5)))) |
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71 |
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72 mapping.setSize(int(m.group(8))) |
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73 mapping.setDirection(m.group(3)) |
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74 |
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75 editString = m.group(10) |
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76 nbMismatches = 0 |
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77 nbGaps = 0 |
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78 while editString != "": |
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79 m = re.search(r"^(\d+)(\D.*)$", editString) |
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80 if m != None: |
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81 editString = m.group(2) |
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82 else: |
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83 m = re.search(r"^(\d+)$", editString) |
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84 if m != None: |
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85 editString = "" |
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86 else: |
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87 m = re.search(r"^([A-Z])(.*)$", editString) |
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88 if m != None: |
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89 nbMismatches += 1 |
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90 editString = m.group(2) |
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91 else: |
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92 m = re.search(r"^\((\w+)\)(.*)$", editString) |
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93 if m != None: |
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94 nbGaps += len(m.group(1)) |
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95 editString = m.group(2) |
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96 else: |
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97 m = re.search(r"^-(.*)$", editString) |
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98 if m != None: |
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99 nbGaps += 1 |
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100 editString = m.group(1) |
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101 else: |
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102 sys.exit("Cannot understand edit string %s from line %s" % (editString, line)) |
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103 |
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104 mapping.setNbMismatches(nbMismatches) |
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105 mapping.setNbGaps(nbGaps) |
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106 |
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107 return mapping |