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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 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
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36 class ExoParser(MapperParser):
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37 """A class that parses the output of Exonerate - roll your own format"""
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38
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39 def __init__(self, fileName, verbosity = 0):
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40 super(ExoParser, 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(ExoParser, 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 ["exo", "exonerate"]
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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 while "Hostname" not in self.handle.readline():
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54 self.currentLineNb += 1
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55 pass
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56
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57
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58 def parseLine(self, line):
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59
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60 if line == "-- completed exonerate analysis\n":
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61 return None
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62
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63 m = re.search(r"^\s*(\S+)\s+(\d+)\s+(\d+)\s+[+-]\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s+(\d+)\s+(\S.*)$", line)
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64 if m == None:
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65 sys.exit("\nLine %d '%s' does not have a RYO format" % (self.currentLineNb, line))
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66
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67 mapping = Mapping()
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68 name = m.group(1)
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69 queryStart = min(int(m.group(2)), int(m.group(3)))
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70 queryEnd = max(int(m.group(2)), int(m.group(3)))-1
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71 chromosome = m.group(4)
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72 targetStart = min(int(m.group(5)), int(m.group(6)))
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73 targetEnd = max(int(m.group(5)), int(m.group(6)))-1
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74 direction = m.group(7)
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75 nbMismatches = int(m.group(8))
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76 rest = m.group(9).strip()
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77
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78 nbGaps = 0
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79 queryOffset = 0
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80 targetOffset = 0
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81
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82 subMapping = None
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83 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest)
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84 while m != None:
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85 queryDistance = int(m.group(2))
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86 targetDistance = int(m.group(3))
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87 if m.group(1) == "M":
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88 if subMapping == None:
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89 subMapping = SubMapping()
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90
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91 subMapping.setSize(queryDistance)
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92 subMapping.setDirection(direction)
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93
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94 subMapping.queryInterval.setName(name)
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95 subMapping.queryInterval.setStart(queryStart + queryOffset)
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96 subMapping.queryInterval.setDirection(direction)
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97
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98 subMapping.targetInterval.setChromosome(chromosome)
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99 subMapping.targetInterval.setStart(targetStart + targetOffset)
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100 subMapping.targetInterval.setDirection(1)
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101
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102 elif m.group(1) == "G":
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103 nbGaps += max(queryDistance, targetDistance)
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104
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105 elif m.group(1) == "I" or m.group(1) == "5" or m.group(1) == "3":
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106 if subMapping != None:
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107 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
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108 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)
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109 mapping.addSubMapping(subMapping)
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110 subMapping = None
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111 else:
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112 sys.exit("Cannot understand sign '%s' in line %s" % (m.group(1), line))
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113
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114 queryOffset += queryDistance
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115 targetOffset += targetDistance
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116 rest = rest[m.end():].strip()
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117 m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest)
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118
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119 if subMapping != None:
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120 subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
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121 subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)
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122 mapping.addSubMapping(subMapping)
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123
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124 mapping.setNbMismatches(nbMismatches)
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125 mapping.setNbGaps(nbGaps)
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126 mapping.setDirection(direction)
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127
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128 mapping.queryInterval.setName(name)
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129 mapping.queryInterval.setStart(queryStart)
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130 mapping.queryInterval.setEnd(queryEnd)
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131
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132 mapping.targetInterval.setChromosome(chromosome)
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133 mapping.targetInterval.setStart(targetStart)
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134 mapping.targetInterval.setEnd(targetEnd)
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135
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136 return mapping
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137
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