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1 #
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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
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