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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 from SMART.Java.Python.structure.SubMapping import SubMapping
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35 from SMART.Java.Python.misc import Utils
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36
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37 class CoordsParser(MapperParser):
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38 """A class that parses the .coords output of Nucmer"""
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39
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40 def __init__(self, fileName, verbosity = 0):
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41 self._lineParseRe = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+\|\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
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42 self._lineParseRe2 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
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43 self._lineParseRe3 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+\|\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
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44 self._lineParseRe4 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
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45 self.lineType = 1
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46 MapperParser.__init__(self, fileName, verbosity)
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47
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48 def getFileFormats():
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49 return ["coords"]
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50 getFileFormats = staticmethod(getFileFormats)
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51
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52 def skipFirstLines(self):
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53 while True:
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54 line = self.handle.readline()
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55 self.currentLineNb += 1
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56 if line == "":
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57 break
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58 if "=====" in line:
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59 break
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60 if "[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]" in line:
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61 self.lineType = 2
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62 break
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63 if "[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]" in line:
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64 self.lineType = 3
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65
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66 if "[% IDY]\t[% SIM]\t[% STP]" in line and "[LEN Q]"in line:
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67 self.lineType = 4
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68 break
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69
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70 def parseLine(self, line):
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71
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72 if self.lineType == 1 :
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73 m = self._lineParseRe.search(line)
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74 elif self.lineType == 2:
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75 m = self._lineParseRe2.search(line)
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76 elif self.lineType == 3:
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77 m = self._lineParseRe3.search(line)
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78 elif self.lineType == 4:
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79 m = self._lineParseRe4.search(line)
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80 if m == None:
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81 sys.exit("\nLine %d '%s' does not have a NucMer format" % (self.currentLineNb, line))
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82
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83 mapping = Mapping()
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84
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85 subMapping = SubMapping()
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86 subMapping.queryInterval.setName(m.group("qName"))
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87 subMapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
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88 subMapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
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89 subMapping.queryInterval.setSize(int(m.group("qLength")))
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90 subMapping.queryInterval.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
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91
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92 subMapping.targetInterval.setChromosome(m.group("tName"))
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93 subMapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
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94 subMapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
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95 subMapping.targetInterval.setSize(int(m.group("tLength")))
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96 subMapping.targetInterval.setDirection(int(m.group("tEnd")) - int(m.group("tStart")))
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97
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98 subMapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
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99 subMapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
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100 subMapping.setIdentity(float(m.group("identity")))
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101
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102 mapping.addSubMapping(subMapping)
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103 mapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
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104 mapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
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105 mapping.targetInterval.setSize(int(m.group("tLength")))
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106 mapping.targetInterval.setChromosome(m.group("tName"))
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107
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108 mapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
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109 mapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
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110 mapping.queryInterval.setSize(int(m.group("qLength")))
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111 mapping.queryInterval.setName(m.group("qName"))
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112 mapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
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113 mapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
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114 mapping.setIdentity(float(m.group("identity")))
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115 mapping.setTagValue("feature", "match")
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116 mapping.setTagValue("Target", "%s %d %d" % (m.group("qName"), int(m.group("qStart")), int(m.group("qEnd"))))
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117
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118 if self.lineType ==2 or self.lineType ==4:
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119 mapping.setTagValue("target_pident", float(m.group("identity")))
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120 mapping.setTagValue("target_pcover", float(m.group("qcov")))
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121 mapping.setTagValue("target_length", int(m.group("qlen")))
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122
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123
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124 # Specific to Mark Work. Commented lines because of possible slowdown.
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125 # for line in self.handle:
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126 # string1 = line.strip()
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127 # self.currentLineNb += 1
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128 # break
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129 # for line in self.handle:
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130 # string2 = line.strip()
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131 # self.currentLineNb += 1
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132 # break
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133 # print(len(string1),len(string2))
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134 # mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
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135 mapping.setNbGaps(0)
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136
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137 return mapping
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