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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 from SMART.Java.Python.structure.Interval import Interval
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36 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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37
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38 class PslParser(MapperParser):
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39 """A class that parses the output of PSL format (of SSAHA and BLAT)"""
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40
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41 def __init__(self, fileName, verbosity = 0):
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42 super(PslParser, self).__init__(fileName, verbosity)
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43
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44
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45 def __del__(self):
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46 super(PslParser, self).__del__()
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47
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48
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49 def getFileFormats():
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50 return ["psl"]
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51 getFileFormats = staticmethod(getFileFormats)
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52
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53
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54 def getInfos(self):
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55 self.chromosomes = set()
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56 self.nbMappings = 0
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57 self.size = 0
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58 self.reset()
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59 progress = UnlimitedProgress(100000, "Getting info on PSL file, # mappings read:", self.verbosity)
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60 for line in self.handle:
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61 progress.inc()
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62 line = line.strip()
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63 if line == "":
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64 continue
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65 parts = line.split("\t")
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66 chromosome = parts[13]
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67 self.chromosomes.add(chromosome)
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68 self.nbMappings += 1
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69 self.size += len(parts[0])
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70 self.reset()
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71 progress.done()
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72
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73
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74 def skipFirstLines(self):
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75 while "------" not in self.handle.readline():
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76 self.currentLineNb += 1
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77 pass
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78
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79 def _computeStarts(self,seqSize,blockSize,start,targetStrand):
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80 if targetStrand == "+":
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81 pass
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82 else:
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83 start = seqSize-blockSize-start
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84 return start
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85
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86
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87
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88 def parseLine(self, line):
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89 m = re.search(r"^\s*(psl:\s+)?(\d+)\s+(\d+)\s+(\d+)\s+\d+\s+\d+\s+(\d+)\s+\d+\s+(\d+)\s+([+-]{1,2})\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s*$", line)
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90 if m == None:
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91 raise Exception("\nLine %d '%s' does not have a PSL format" % (self.currentLineNb, line))
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92
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93 mapping = Mapping()
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94
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95 queryStrand = m.group(7)[0]
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96
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97 if len(m.group(7)) == 1:
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98 targetStrand = "+"
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99 else:
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100 targetStrand = m.group(7)[1]
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101
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102
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103 for i in range(0, int(m.group(16))):
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104 size = int(m.group(17).split(",")[i])
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105 queryStart = int(m.group(18).split(",")[i])
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106 targetStart = int(m.group(19).split(",")[i])
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107 querySize = int(m.group(9))
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108 targetSize = int(m.group(13))
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109
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110 subMapping = SubMapping()
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111 subMapping.setSize(size)
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112 subMapping.setDirection(m.group(7)[0])
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113
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114 queryInterval = Interval()
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115 targetInterval = Interval()
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116
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117 queryInterval.setName(m.group(8))
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118 queryStart = self._computeStarts(querySize,size,queryStart,targetStrand)
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119 queryInterval.setStart(queryStart + 1)
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120 queryInterval.setEnd(queryStart + size)
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121 queryInterval.setDirection(queryStrand)
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122
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123 targetInterval.setChromosome(m.group(12))
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124 targetStart = self._computeStarts(targetSize,size,targetStart,targetStrand)
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125 targetInterval.setStart(targetStart + 1)
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126 targetInterval.setEnd(targetStart + size)
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127 targetInterval.setDirection(targetStrand)
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128
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129 subMapping.setQueryInterval(queryInterval)
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130 subMapping.setTargetInterval(targetInterval)
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131 mapping.addSubMapping(subMapping)
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132
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133 mapping.setSize(int(m.group(2)) + int(m.group(3)) + int(m.group(4)))
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134 mapping.setNbMismatches(int(m.group(3)) + int(m.group(4)))
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135 mapping.setNbGaps(int(m.group(5)))
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136 mapping.setDirection(queryStrand)
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137
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138 queryInterval = Interval()
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139 targetInterval = Interval()
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140
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141 queryInterval.setName(m.group(8))
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142 queryInterval.setStart(min(int(m.group(10)), int(m.group(11))))
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143 queryInterval.setEnd( max(int(m.group(10)), int(m.group(11))))
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144 queryInterval.setDirection(queryStrand)
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145
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146 targetInterval.setChromosome(m.group(12))
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147 targetInterval.setStart(min(int(m.group(14))+1, int(m.group(15))))
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148 targetInterval.setEnd( max(int(m.group(14))+1, int(m.group(15))))
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149 targetInterval.setDirection(targetStrand)
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150
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151 mapping.setQueryInterval(queryInterval)
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152 mapping.setTargetInterval(targetInterval)
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153
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154 return mapping
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155
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