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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 sys
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31 from commons.core.parsing.MapperParser import MapperParser
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32 from SMART.Java.Python.structure import Mapping
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33
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34 class ElandParser(MapperParser):
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35 """A class that parses ELAND format"""
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36
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37 def __init__(self, fileName, verbosity = 0):
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38 super(ElandParser, self).__init__(fileName, verbosity)
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39
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40
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41 def __del__(self):
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42 super(ElandParser, self).__del__()
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43
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44
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45 def getFileFormats():
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46 return ["eland"]
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47 getFileFormats = staticmethod(getFileFormats)
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48
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49
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50 def skipFirstLines(self):
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51 pass
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52
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53
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54 def getInfos(self):
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55 super(ElandParser, self).getInfos()
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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 line = line.strip()
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61
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62 fields = line.split("\t")
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63 if len(fields) < 22:
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64 sys.exit("Line %d '%s' does not look like a ELAND line (number of fields is %d instead of 22)" % (self.currentLineNb, line, len(fields)))
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65
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66 flowCell = fields[0]
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67 run = fields[1]
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68 lane = fields[2]
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69 tile = fields[3]
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70 xcoord = fields[4]
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71 ycoord = fields[5]
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72 index = fields[6]
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73 number = fields[7]
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74 read = fields[8]
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75 quality = fields[9]
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76 chromosome = fields[10]
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77 contig = fields[11]
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78 position = fields[12]
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79 strand = fields[13]
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80 description = fields[14]
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81 singleScore = fields[15]
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82 pairScore = fields[16]
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83 partnerChromosome = fields[17]
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84 partnerContig = fields[18]
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85 partnerOffset = fields[19]
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86 partnerStrand = fields[20]
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87 filtering = fields[21]
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88
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89 if number != "1":
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90 sys.exit("S-MART cannot handle pair-end reads yet!")
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91
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92 # nothing found
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93 if position == "":
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94 return None
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95
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96 name = "%s_%s:%s:%s:%s:%s#0/1" % (flowCell, run, lane, tile, xcoord, ycoord)
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97 direction = 1 if strand == "F" else -1
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98 nbMismatches = 0
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99 for char in description:
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100 if ord("A") <= ord(char) and ord(char) <= ord("Z"):
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101 nbMismatches += 1
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102
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103 mapping = Mapping()
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104 mapping.setTagValue("qualityString", quality)
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105
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106 mapping.queryInterval.setName(name)
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107 mapping.queryInterval.setDirection(direction)
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108 mapping.queryInterval.setStart(1)
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109 mapping.queryInterval.setEnd(len(read))
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110
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111 mapping.targetInterval.setChromosome(chromosome)
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112 mapping.targetInterval.setStart(int(position))
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113 mapping.targetInterval.setEnd(int(position) + len(read))
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114 mapping.targetInterval.setDirection(1)
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115
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116 mapping.setSize(len(read))
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117 mapping.setDirection(direction)
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118
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119 mapping.setNbGaps(0)
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120 mapping.setNbMismatches(nbMismatches)
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121 mapping.setTagValue("score", int(singleScore))
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122
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123 if filtering == "Y":
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124 return mapping
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125 # mapping filtered out
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126 return None
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