Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/AxtParser.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
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26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 from SMART.Java.Python.structure.SubMapping import SubMapping
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34 from commons.core.parsing.MapperParser import MapperParser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 from SMART.Java.Python.misc import Utils
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36 from SMART.Java.Python.misc.Utils import getHammingDistance
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37
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38
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39 class AxtParser(MapperParser):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 """A class that parses AXT (as given by Mosaik)"""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41
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42 def __init__(self, fileName, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 super(AxtParser, self).__init__(fileName, verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 self.queryLine = None
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45 self.subjectLine = None
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46
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47 def __del__(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 super(AxtParser, self).__del__()
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49
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50
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51 def getFileFormats():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 return ["axt"]
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53 getFileFormats = staticmethod(getFileFormats)
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54
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55
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56 def skipFirstLines(self):
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57 pass
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58
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59
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60 def getInfos(self):
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61 self.chromosomes = set()
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62 self.nbMappings = 0
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63 self.size = 0
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64 cpt = 0
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65 self.reset()
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66 for line in self.handle:
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67 line = line.strip()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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68 if line == "": continue
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69 if cpt % 3 == 0:
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70 line = line.strip()
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71 parts = line.split(" ")
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72 self.chromosomes.add(parts[1])
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73 self.size += int(parts[6])
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74 self.nbMappings += 1
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75 cpt += 1
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76 if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
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77 sys.stdout.write(" %d mappings read\r" % (self.nbMappings))
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78 sys.stdout.flush()
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79 self.reset()
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80 if self.verbosity >= 10:
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81 print " %d mappings read" % (self.nbMappings)
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82 print "Done."
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83
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84
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85 def parseLine(self, line):
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86
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87 if line.strip() == "":
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88 for line in self.handle:
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89 self.currentLineNb += 1
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90 break
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91 if line.strip() == "":
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92 return None
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93
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94 m = re.search(r"^\s*\d+\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s*$", line)
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95 if m != None:
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96 #sys.exit("\nLine %d '%s' does not have an AXT format" % (self.currentLineNb, line))
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97
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98 mapping = Mapping()
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99 subMapping = SubMapping()
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100
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101 offset = -1 if m.group(7) == "-" else 0
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102 subMapping.queryInterval.setName(m.group(4))
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103 subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
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104 subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
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105 subMapping.queryInterval.setDirection(m.group(7))
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106
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107 subMapping.targetInterval.setChromosome(m.group(1))
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108 subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
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109 subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
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110 subMapping.targetInterval.setDirection(1)
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111
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112 subMapping.setSize(min(subMapping.targetInterval.getSize(), subMapping.queryInterval.getSize()))
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113 subMapping.setDirection(m.group(7))
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114
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115 mapping.addSubMapping(subMapping)
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116
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117 mapping.setDirection(m.group(7))
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118 mapping.targetInterval.setChromosome(m.group(1))
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119 mapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
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120 mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
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121
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122 mapping.queryInterval.setName(m.group(4))
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123 mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
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124 mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
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125
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126 mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize()))
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127
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128 for line in self.handle:
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129 string1 = line.strip()
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130 self.currentLineNb += 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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131 break
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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132 for line in self.handle:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 string2 = line.strip()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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134 self.currentLineNb += 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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135 break
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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136 mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 mapping.setNbGaps(0)
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138
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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139 self.currentMapping = mapping
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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140 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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141 if self.queryLine == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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142 self.queryLine = line
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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143 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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144 self.subjectLine = line
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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145 seqLen = float(len(self.subjectLine))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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146 dist = float(getHammingDistance(self.queryLine, self.subjectLine))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
147 identity = ((seqLen-dist)/seqLen) *100
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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148 self.currentMapping.setIdentity(identity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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149 self.queryLine = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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150 self.subjectLine = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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151 return self.currentMapping
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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152
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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153
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
154