Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/PathUtils.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 |
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31 |
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32 import os |
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33 import sys |
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34 import copy |
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35 from commons.core.coord.Path import Path |
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36 from commons.core.coord.SetUtils import SetUtils |
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37 from commons.core.coord.Map import Map |
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38 from commons.core.coord.AlignUtils import AlignUtils |
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39 from commons.core.checker.RepetException import RepetDataException |
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40 |
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41 ## Static methods for the manipulation of Path instances |
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42 # |
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43 class PathUtils ( object ): |
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44 |
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45 ## Change the identifier of each Set instance in the given list |
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46 # |
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47 # @param lPaths list of Path instances |
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48 # @param newId new identifier |
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49 # |
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50 def changeIdInList(lPaths, newId): |
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51 for iPath in lPaths: |
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52 iPath.id = newId |
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53 |
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54 changeIdInList = staticmethod( changeIdInList ) |
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55 |
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56 |
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57 ## Return a list of Set instances containing the query range from a list of Path instances |
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58 # |
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59 # @param lPaths a list of Path instances |
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60 # |
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61 def getSetListFromQueries(lPaths): |
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62 lSets = [] |
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63 for iPath in lPaths: |
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64 lSets.append( iPath.getSubjectAsSetOfQuery() ) |
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65 return lSets |
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66 |
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67 getSetListFromQueries = staticmethod( getSetListFromQueries ) |
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68 |
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69 #TODO: add tests !!!! |
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70 ## Return a list of Set instances containing the query range from a list of Path instances |
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71 # |
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72 # @param lPaths a list of Path instances |
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73 # |
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74 @staticmethod |
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75 def getSetListFromSubjects(lPaths): |
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76 lSets = [] |
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77 for iPath in lPaths: |
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78 lSets.append( iPath.getQuerySetOfSubject() ) |
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79 return lSets |
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80 |
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81 |
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82 ## Return a sorted list of Range instances containing the subjects from a list of Path instances |
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83 # |
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84 # @param lPaths a list of Path instances |
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85 # @note meaningful only if all Path instances have same identifier |
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86 # |
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87 def getRangeListFromSubjects( lPaths ): |
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88 lRanges = [] |
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89 for iPath in lPaths: |
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90 lRanges.append( iPath.range_subject ) |
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91 if lRanges[0].isOnDirectStrand(): |
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92 return sorted( lRanges, key=lambda iRange: ( iRange.getMin(), iRange.getMax() ) ) |
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93 else: |
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94 return sorted( lRanges, key=lambda iRange: ( iRange.getMax(), iRange.getMin() ) ) |
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95 |
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96 getRangeListFromSubjects = staticmethod( getRangeListFromSubjects ) |
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97 |
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98 |
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99 ## Return a tuple with min and max of query coordinates from Path instances in the given list |
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100 # |
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101 # @param lPaths a list of Path instances |
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102 # |
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103 def getQueryMinMaxFromPathList(lPaths): |
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104 qmin = -1 |
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105 qmax = -1 |
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106 for iPath in lPaths: |
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107 if qmin == -1: |
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108 qmin = iPath.range_query.start |
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109 qmin = min(qmin, iPath.range_query.getMin()) |
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110 qmax = max(qmax, iPath.range_query.getMax()) |
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111 return (qmin, qmax) |
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112 |
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113 getQueryMinMaxFromPathList = staticmethod( getQueryMinMaxFromPathList ) |
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114 |
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115 |
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116 ## Return a tuple with min and max of subject coordinates from Path instances in the given list |
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117 # |
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118 # @param lPaths lists of Path instances |
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119 # |
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120 def getSubjectMinMaxFromPathList(lPaths): |
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121 smin = -1 |
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122 smax = -1 |
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123 for iPath in lPaths: |
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124 if smin == -1: |
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125 smin = iPath.range_subject.start |
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126 smin = min(smin, iPath.range_subject.getMin()) |
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127 smax = max(smax, iPath.range_subject.getMax()) |
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128 return (smin, smax) |
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129 |
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130 getSubjectMinMaxFromPathList = staticmethod( getSubjectMinMaxFromPathList ) |
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131 |
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132 |
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133 ## Return True if the query range of any Path instance from the first list overlaps with the query range of any Path instance from the second list |
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134 # |
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135 # @param lPaths1: list of Path instances |
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136 # @param lPaths2: list of Path instances |
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137 # @return boolean |
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138 # |
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139 def areQueriesOverlappingBetweenPathLists( lPaths1, lPaths2 ): |
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140 lSortedPaths1 = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths1 ) |
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141 lSortedPaths2 = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths2 ) |
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142 i = 0 |
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143 j = 0 |
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144 while i != len(lSortedPaths1): |
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145 while j != len(lSortedPaths2): |
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146 if not lSortedPaths1[i].range_query.isOverlapping( lSortedPaths2[j].range_query ): |
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147 j += 1 |
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148 else: |
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149 return True |
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150 i += 1 |
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151 return False |
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152 |
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153 areQueriesOverlappingBetweenPathLists = staticmethod( areQueriesOverlappingBetweenPathLists ) |
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154 |
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155 |
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156 ## Show Path instances contained in the given list |
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157 # |
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158 # @param lPaths a list of Path instances |
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159 # |
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160 def showList(lPaths): |
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161 for iPath in lPaths: |
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162 iPath.show() |
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163 |
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164 showList = staticmethod( showList ) |
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165 |
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166 |
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167 ## Write Path instances contained in the given list |
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168 # |
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169 # @param lPaths a list of Path instances |
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170 # @param fileName name of the file to write the Path instances |
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171 # @param mode the open mode of the file ""w"" or ""a"" |
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172 # |
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173 def writeListInFile(lPaths, fileName, mode="w"): |
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174 AlignUtils.writeListInFile(lPaths, fileName, mode) |
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175 |
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176 writeListInFile = staticmethod( writeListInFile ) |
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177 |
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178 |
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179 ## Return new list of Path instances with no duplicate |
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180 # |
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181 # @param lPaths a list of Path instances |
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182 # @param useOnlyCoord boolean if True, check only coordinates and sequence names |
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183 # @return lUniqPaths a path instances list |
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184 # |
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185 def getPathListWithoutDuplicates(lPaths, useOnlyCoord = False): |
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186 if len(lPaths) < 2: |
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187 return lPaths |
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188 lSortedPaths = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier( lPaths ) |
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189 lUniqPaths = [ lSortedPaths[0] ] |
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190 if useOnlyCoord: |
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191 for iPath in lSortedPaths[1:]: |
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192 if iPath.range_query.start != lUniqPaths[-1].range_query.start \ |
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193 or iPath.range_query.end != lUniqPaths[-1].range_query.end \ |
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194 or iPath.range_query.seqname != lUniqPaths[-1].range_query.seqname \ |
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195 or iPath.range_subject.start != lUniqPaths[-1].range_subject.start \ |
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196 or iPath.range_subject.end != lUniqPaths[-1].range_subject.end \ |
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197 or iPath.range_subject.seqname != lUniqPaths[-1].range_subject.seqname: |
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198 lUniqPaths.append( iPath ) |
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199 else: |
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200 for iPath in lSortedPaths[1:]: |
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201 if iPath != lUniqPaths[-1]: |
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202 lUniqPaths.append( iPath ) |
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203 return lUniqPaths |
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204 |
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205 getPathListWithoutDuplicates = staticmethod( getPathListWithoutDuplicates ) |
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206 |
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207 |
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208 def getPathListWithoutDuplicatesOnQueryCoord(lPaths): |
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209 if len(lPaths) < 2: |
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210 return lPaths |
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211 lSortedPaths = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier( lPaths ) |
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212 lUniqPaths = [ lSortedPaths[0] ] |
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213 for iPath in lSortedPaths[1:]: |
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214 if iPath.range_query.start != lUniqPaths[-1].range_query.start \ |
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215 or iPath.range_query.end != lUniqPaths[-1].range_query.end \ |
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216 or iPath.range_query.seqname != lUniqPaths[-1].range_query.seqname: |
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217 lUniqPaths.append( iPath ) |
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218 return lUniqPaths |
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219 |
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220 getPathListWithoutDuplicatesOnQueryCoord = staticmethod(getPathListWithoutDuplicatesOnQueryCoord) |
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221 |
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222 |
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223 ## Split a Path list in several Path lists according to the identifier |
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224 # |
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225 # @param lPaths a list of Path instances |
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226 # @return a dictionary which keys are identifiers and values Path lists |
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227 # |
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228 def getDictOfListsWithIdAsKey( lPaths ): |
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229 dId2PathList = {} |
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230 for iPath in lPaths: |
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231 if dId2PathList.has_key( iPath.id ): |
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232 dId2PathList[ iPath.id ].append( iPath ) |
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233 else: |
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234 dId2PathList[ iPath.id ] = [ iPath ] |
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235 return dId2PathList |
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236 |
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237 getDictOfListsWithIdAsKey = staticmethod( getDictOfListsWithIdAsKey ) |
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238 |
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239 |
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240 ## Split a Path file in several Path lists according to the identifier |
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241 # |
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242 # @param pathFile name of the input Path file |
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243 # @return a dictionary which keys are identifiers and values Path lists |
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244 # |
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245 def getDictOfListsWithIdAsKeyFromFile( pathFile ): |
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246 dId2PathList = {} |
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247 pathFileHandler = open( pathFile, "r" ) |
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248 while True: |
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249 line = pathFileHandler.readline() |
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250 if line == "": |
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251 break |
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252 iPath = Path() |
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253 iPath.setFromString( line ) |
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254 if dId2PathList.has_key( iPath.id ): |
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255 dId2PathList[ iPath.id ].append( iPath ) |
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256 else: |
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257 dId2PathList[ iPath.id ] = [ iPath ] |
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258 pathFileHandler.close() |
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259 return dId2PathList |
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260 |
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261 getDictOfListsWithIdAsKeyFromFile = staticmethod( getDictOfListsWithIdAsKeyFromFile ) |
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262 |
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263 |
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264 ## Return a list of Path list(s) obtained while splitting a list of connected Path instances according to another based on query coordinates |
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265 # |
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266 # @param lToKeep: a list of Path instances to keep (reference) |
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267 # @param lToUnjoin: a list of Path instances to unjoin |
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268 # @return: list of Path list(s) (can be empty if one of the input lists is empty) |
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269 # @warning: all the path instances in a given list MUST be connected (i.e. same identifier) |
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270 # @warning: all the path instances in a given list MUST NOT overlap neither within each other nor with the Path instances of the other list |
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271 # |
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272 def getPathListUnjoinedBasedOnQuery( lToKeep, lToUnjoin ): |
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273 lSortedToKeep = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lToKeep ) |
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274 lSortedToUnjoin = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lToUnjoin ) |
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275 if lToUnjoin == []: |
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276 return [] |
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277 if lToKeep == []: |
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278 return [ lToUnjoin ] |
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279 |
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280 lLists = [] |
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281 k = 0 |
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282 while k < len(lSortedToKeep): |
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283 j1 = 0 |
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284 while j1 < len(lSortedToUnjoin) and lSortedToKeep[k].range_query.getMin() > lSortedToUnjoin[j1].range_query.getMax(): |
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285 j1 += 1 |
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286 if j1 == len(lSortedToUnjoin): |
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287 break |
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288 if j1 != 0: |
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289 lLists.append( lSortedToUnjoin[:j1] ) |
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290 del lSortedToUnjoin[:j1] |
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291 j1 = 0 |
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292 if k+1 == len(lSortedToKeep): |
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293 break |
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294 j2 = j1 |
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295 if j2 < len(lSortedToUnjoin) and lSortedToKeep[k+1].range_query.getMin() > lSortedToUnjoin[j2].range_query.getMax(): |
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296 while j2 < len(lSortedToUnjoin) and lSortedToKeep[k+1].range_query.getMin() > lSortedToUnjoin[j2].range_query.getMax(): |
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297 j2 += 1 |
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298 lLists.append( lSortedToUnjoin[j1:j2] ) |
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299 del lSortedToUnjoin[j1:j2] |
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300 k += 1 |
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301 |
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302 if lLists != [] or k == 0: |
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303 lLists.append( lSortedToUnjoin ) |
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304 return lLists |
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305 |
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306 getPathListUnjoinedBasedOnQuery = staticmethod( getPathListUnjoinedBasedOnQuery ) |
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307 |
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308 |
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309 ## Return the identity of the Path list, the identity of each instance being weighted by the length of each query range |
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310 # All Paths should have the same query and subject. |
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311 # The Paths are merged using query coordinates only. |
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312 # |
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313 # @param lPaths list of Path instances |
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314 # |
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315 def getIdentityFromPathList( lPaths, checkSubjects=True ): |
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316 if len( PathUtils.getListOfDistinctQueryNames( lPaths ) ) > 1: |
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317 msg = "ERROR: try to compute identity from Paths with different queries" |
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318 sys.stderr.write( "%s\n" % msg ) |
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319 sys.stderr.flush() |
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320 raise Exception |
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321 if checkSubjects and len( PathUtils.getListOfDistinctSubjectNames( lPaths ) ) > 1: |
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322 msg = "ERROR: try to compute identity from Paths with different subjects" |
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323 sys.stderr.write( "%s\n" % msg ) |
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324 sys.stderr.flush() |
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325 raise Exception |
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326 identity = 0 |
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327 lMergedPaths = PathUtils.mergePathsInListUsingQueryCoordsOnly( lPaths ) |
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328 lQuerySets = PathUtils.getSetListFromQueries( lMergedPaths ) |
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329 lMergedQuerySets = SetUtils.mergeSetsInList( lQuerySets ) |
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330 totalLengthOnQry = SetUtils.getCumulLength( lMergedQuerySets ) |
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331 for iPath in lMergedPaths: |
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332 identity += iPath.identity * iPath.getLengthOnQuery() |
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333 weightedIdentity = identity / float(totalLengthOnQry) |
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334 if weightedIdentity < 0: |
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335 msg = "ERROR: weighted identity '%.2f' outside range" % weightedIdentity |
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336 sys.stderr.write("%s\n" % msg) |
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337 sys.stderr.flush() |
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338 raise Exception |
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339 elif weightedIdentity > 100: |
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340 msg = "ERROR: weighted identity '%.2f' outside range" % weightedIdentity |
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341 sys.stderr.write("%s\n" % msg) |
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342 sys.stderr.flush() |
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343 raise RepetDataException(msg) |
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344 return weightedIdentity |
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345 |
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346 getIdentityFromPathList = staticmethod( getIdentityFromPathList ) |
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347 |
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348 |
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349 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, and finally their initial order. |
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350 # |
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351 # @param lPaths list of Path instances |
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352 # |
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353 def getPathListSortedByIncreasingMinQueryThenMaxQuery(lPaths): |
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354 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), iPath.getQueryMax() ) ) |
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355 |
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356 getPathListSortedByIncreasingMinQueryThenMaxQuery = staticmethod( getPathListSortedByIncreasingMinQueryThenMaxQuery ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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358 |
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359 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, then their identifier, and finally their initial order. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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360 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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361 # @param lPaths list of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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362 # |
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363 def getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier(lPaths): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), iPath.getQueryMax(), iPath.getIdentifier() ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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365 |
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366 getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier = staticmethod( getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier ) |
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367 |
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368 |
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369 ## Return a list of Path instances sorted in increasing order according to the min of the query, then the max of the query, then the min of the subject, then the max of the subject and finally their initial order. |
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370 # |
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371 # @param lPaths list of Path instances |
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372 # |
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373 @staticmethod |
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374 def getPathListSortedByIncreasingMinQueryThenMaxQueryThenMinSubjectThenMaxSubject(lPaths): |
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375 return sorted(lPaths, key=lambda iPath: (iPath.getQueryMin(), iPath.getQueryMax(), iPath.getSubjectMin(), iPath.getSubjectMax())) |
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376 |
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377 |
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378 ## Return a list of the distinct identifiers |
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379 # |
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380 # @param lPaths list of Path instances |
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381 # |
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382 def getListOfDistinctIdentifiers( lPaths ): |
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383 sDistinctIdentifiers = set() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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384 for iPath in lPaths: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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385 sDistinctIdentifiers.add(iPath.id) |
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386 return list(sDistinctIdentifiers) |
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387 |
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388 getListOfDistinctIdentifiers = staticmethod( getListOfDistinctIdentifiers ) |
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389 |
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390 |
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391 ## Return a list of the distinct query names present in the collection |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 # |
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393 # @param lPaths list of Path instances |
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394 # |
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395 def getListOfDistinctQueryNames( lPaths ): |
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396 sDistinctQueryNames = set() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 for iPath in lPaths: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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398 sDistinctQueryNames.add(iPath.range_query.seqname) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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399 return list(sDistinctQueryNames) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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401 getListOfDistinctQueryNames = staticmethod( getListOfDistinctQueryNames ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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404 ## Return a list of the distinct subject names present in the collection |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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405 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 # @param lPaths list of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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407 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 def getListOfDistinctSubjectNames( lPaths ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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409 sDistinctSubjectNames = set() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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410 for iPath in lPaths: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 sDistinctSubjectNames.add(iPath.range_subject.seqname) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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412 return list(sDistinctSubjectNames) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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413 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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414 getListOfDistinctSubjectNames = staticmethod( getListOfDistinctSubjectNames ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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415 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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416 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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417 ## Return a list of lists containing query coordinates of the connections sorted in increasing order. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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418 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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419 # @param lConnectedPaths: list of Path instances having the same identifier |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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420 # @param minLength: threshold below which connections are not reported (default= 0 bp) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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421 # @note: return only connections longer than threshold |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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422 # @note: if coordinate on query ends at 100, return 101 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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423 # @warning: Path instances MUST be sorted in increasing order according to query coordinates |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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424 # @warning: Path instances MUST be on direct query strand (and maybe on reverse subject strand) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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425 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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426 def getListOfJoinCoordinatesOnQuery(lConnectedPaths, minLength=0): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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427 lJoinCoordinates = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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428 for i in xrange(1,len(lConnectedPaths)): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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429 startJoin = lConnectedPaths[i-1].range_query.end |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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430 endJoin = lConnectedPaths[i].range_query.start |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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431 if endJoin - startJoin + 1 > minLength: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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432 lJoinCoordinates.append( [ startJoin + 1, endJoin - 1 ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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433 return lJoinCoordinates |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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434 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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435 getListOfJoinCoordinatesOnQuery = staticmethod( getListOfJoinCoordinatesOnQuery ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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436 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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437 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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438 ## Return the length on the query of all Path instance in the given list |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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439 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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440 # @param lPaths list of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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441 # @note overlapping ranges are not summed but truncated. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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442 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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443 def getLengthOnQueryFromPathList( lPaths ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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444 lSets = PathUtils.getSetListFromQueries( lPaths ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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445 lMergedSets = SetUtils.mergeSetsInList( lSets ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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446 length = SetUtils.getCumulLength( lMergedSets ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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447 return length |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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448 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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449 getLengthOnQueryFromPathList = staticmethod( getLengthOnQueryFromPathList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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450 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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451 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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452 ## Convert a Path file into an Align file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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453 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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454 # @param pathFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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455 # @param alignFile: name of the output Align file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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456 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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457 def convertPathFileIntoAlignFile(pathFile, alignFile): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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458 pathFileHandler = open( pathFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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459 alignFileHandler = open( alignFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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460 iPath = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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461 while True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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462 line = pathFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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463 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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464 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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465 iPath.setFromString( line ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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466 iAlign = iPath.getAlignInstance() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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467 iAlign.write( alignFileHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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468 pathFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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469 alignFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
470 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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471 convertPathFileIntoAlignFile = staticmethod( convertPathFileIntoAlignFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
472 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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473 #TODO: duplicated method => to rename with the name of the next method (which is called) ? |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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474 ## Convert a Path File into a Map file with query coordinates only |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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475 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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476 # @param pathFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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477 # @param mapFile: name of the output Map file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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478 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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479 def convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, mapFile ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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480 pathFileHandler = open( pathFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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481 mapFileHandler = open( mapFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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482 p = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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483 while True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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484 line = pathFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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485 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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486 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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487 p.reset() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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488 p.setFromTuple( line.split("\t") ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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489 p.writeSubjectAsMapOfQuery( mapFileHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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490 pathFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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491 mapFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
492 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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493 convertPathFileIntoMapFileWithQueryCoordsOnly = staticmethod( convertPathFileIntoMapFileWithQueryCoordsOnly ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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494 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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495 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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496 ## for each line of a given Path file, write the coordinates of the subject on the query as one line in a Map file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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497 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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498 # @param pathFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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499 # @param mapFile: name of the output Map file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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500 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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501 def convertPathFileIntoMapFileWithSubjectsOnQueries( pathFile, mapFile ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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502 PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, mapFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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503 convertPathFileIntoMapFileWithSubjectsOnQueries = staticmethod( convertPathFileIntoMapFileWithSubjectsOnQueries ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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504 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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505 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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506 ## Merge matches on queries |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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507 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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508 # @param inFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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509 # @param outFile: name of the output Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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510 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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511 def mergeMatchesOnQueries(inFile, outFile): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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512 mapFile = "%s.map" % ( inFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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513 PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( inFile, mapFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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514 cmd = "mapOp" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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515 cmd += " -q %s" % ( mapFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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516 cmd += " -m" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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517 cmd += " 2>&1 > /dev/null" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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518 exitStatus = os.system( cmd ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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519 if exitStatus != 0: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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520 print "ERROR: mapOp returned %i" % ( exitStatus ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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521 sys.exit(1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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522 os.remove( mapFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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523 mergeFile = "%s.merge" % ( mapFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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524 mergeFileHandler = open( mergeFile, "r" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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525 outFileHandler = open( outFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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526 m = Map() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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527 while True: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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528 line = mergeFileHandler.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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529 if line == "": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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530 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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531 m.reset() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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532 m.setFromString( line, "\t" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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533 m.writeAsQueryOfPath( outFileHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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534 mergeFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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535 os.remove( mergeFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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536 outFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
537 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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538 mergeMatchesOnQueries = staticmethod( mergeMatchesOnQueries ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
539 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
540 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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541 ## Filter chains of Path(s) which length is below a given threshold |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
542 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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543 # @param lPaths: list of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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544 # @param minLengthChain: minimum length of a chain to be kept |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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545 # @note: a chain may contain a single Path instance |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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546 # @return: a list of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
547 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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548 def filterPathListOnChainLength( lPaths, minLengthChain ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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549 lFilteredPaths = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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550 dPathnum2Paths = PathUtils.getDictOfListsWithIdAsKey( lPaths ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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551 for pathnum in dPathnum2Paths.keys(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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552 length = PathUtils.getLengthOnQueryFromPathList( dPathnum2Paths[ pathnum ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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553 if length >= minLengthChain: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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554 lFilteredPaths += dPathnum2Paths[ pathnum ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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555 return lFilteredPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
556 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
557 filterPathListOnChainLength = staticmethod( filterPathListOnChainLength ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
559 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
560 ## Return a Path list from a Path file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
562 # @param pathFile string name of a Path file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
563 # @return a list of Path instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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564 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
565 def getPathListFromFile( pathFile ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
566 lPaths = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 pathFileHandler = open( pathFile, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
568 while True: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 line = pathFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 if line == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 break |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 iPath = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 iPath.setFromString( line ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
574 lPaths.append( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 pathFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
576 return lPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
578 getPathListFromFile = staticmethod( getPathListFromFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 ## Convert a chain into a 'pathrange' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 # @param lPaths a list of Path instances with the same identifier |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 # @note: the min and max of each Path is used |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 def convertPathListToPathrange( lPaths ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 if len(lPaths) == 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 return |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 if len(lPaths) == 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 return lPaths[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 iPathrange = copy.deepcopy( lPaths[0] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 iPathrange.identity = lPaths[0].identity * lPaths[0].getLengthOnQuery() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 cumulQueryLength = iPathrange.getLengthOnQuery() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 for iPath in lPaths[1:]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 if iPath.id != iPathrange.id: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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596 msg = "ERROR: two Path instances in the chain have different identifiers" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
597 sys.stderr.write( "%s\n" % ( msg ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
598 sys.exit(1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
599 if iPathrange.range_subject.isOnDirectStrand() != iPath.range_subject.isOnDirectStrand(): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 msg = "ERROR: two Path instances in the chain are on different strands" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
601 sys.stderr.write( "%s\n" % ( msg ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
602 sys.exit(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 iPathrange.range_query.start = min( iPathrange.range_query.start, iPath.range_query.start ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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604 iPathrange.range_query.end = max( iPathrange.range_query.end, iPath.range_query.end ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 if iPathrange.range_subject.isOnDirectStrand(): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 iPathrange.range_subject.start = min( iPathrange.range_subject.start, iPath.range_subject.start ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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607 iPathrange.range_subject.end = max( iPathrange.range_subject.end, iPath.range_subject.end ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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608 else: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 iPathrange.range_subject.start = max( iPathrange.range_subject.start, iPath.range_subject.start ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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610 iPathrange.range_subject.end = min( iPathrange.range_subject.end, iPath.range_subject.end ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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611 iPathrange.e_value = min( iPathrange.e_value, iPath.e_value ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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612 iPathrange.score += iPath.score |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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613 iPathrange.identity += iPath.identity * iPath.getLengthOnQuery() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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614 cumulQueryLength += iPath.getLengthOnQuery() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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615 iPathrange.identity = iPathrange.identity / float(cumulQueryLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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616 return iPathrange |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
617 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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618 convertPathListToPathrange = staticmethod( convertPathListToPathrange ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
620 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
621 ## Convert a Path file into an Align file via 'pathrange' |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
622 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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623 # @param pathFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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624 # @param alignFile: name of the output Align file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
625 # @param verbose integer verbosity level |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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626 # @note: the min and max of each Path is used |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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627 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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628 def convertPathFileIntoAlignFileViaPathrange( pathFile, alignFile, verbose=0 ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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629 lPaths = PathUtils.getPathListFromFile( pathFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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630 dId2PathList = PathUtils.getDictOfListsWithIdAsKey( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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631 lIds = dId2PathList.keys() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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632 lIds.sort() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
634 msg = "number of chains: %i" % ( len(lIds) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
635 sys.stdout.write( "%s\n" % ( msg ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
636 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 alignFileHandler = open( alignFile, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 for identifier in lIds: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 iPath = PathUtils.convertPathListToPathrange( dId2PathList[ identifier ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 iAlign = iPath.getAlignInstance() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
641 iAlign.write( alignFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
642 alignFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 convertPathFileIntoAlignFileViaPathrange = staticmethod( convertPathFileIntoAlignFileViaPathrange ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
647 ## Split a list of Path instances according to the name of the query |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
648 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
649 # @param lInPaths list of align instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 # @return lOutPathLists list of align instances lists |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 def splitPathListByQueryName( lInPaths ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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653 lInSortedPaths = sorted( lInPaths, key=lambda o: o.range_query.seqname ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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654 lOutPathLists = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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655 if len(lInSortedPaths) != 0 : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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656 lPathsForCurrentQuery = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
657 previousQuery = lInSortedPaths[0].range_query.seqname |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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658 for iPath in lInSortedPaths : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
659 currentQuery = iPath.range_query.seqname |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
660 if previousQuery != currentQuery : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
661 lOutPathLists.append( lPathsForCurrentQuery ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 previousQuery = currentQuery |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 lPathsForCurrentQuery = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 lPathsForCurrentQuery.append( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 lOutPathLists.append(lPathsForCurrentQuery) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
668 return lOutPathLists |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
669 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
670 splitPathListByQueryName = staticmethod( splitPathListByQueryName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 ## Create an Path file from each list of Path instances in the input list |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 # @param lPathList list of lists with Path instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
676 # @param pattern string |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 # @param dirName string |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
678 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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679 def createPathFiles( lPathList, pattern, dirName="" ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
680 nbFiles = len(lPathList) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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681 countFile = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
682 if dirName != "" : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 if dirName[-1] != "/": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
684 dirName = dirName + '/' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
685 os.mkdir( dirName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 for lPath in lPathList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
688 fileName = dirName + pattern + "_%s.path" % ( str(countFile).zfill( len(str(nbFiles)) ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 PathUtils.writeListInFile( lPath, fileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
690 countFile += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 createPathFiles = staticmethod( createPathFiles ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 ## Return a list of Path instances sorted in increasing order according to the min, then the inverse of the query length, and finally their initial order |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
696 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 # @param lPaths: list of Path instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
699 def getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
700 return sorted( lPaths, key=lambda iPath: ( iPath.getQueryMin(), 1 / float(iPath.getLengthOnQuery()) ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 getPathListSortedByIncreasingQueryMinThenInvQueryLength = staticmethod( getPathListSortedByIncreasingQueryMinThenInvQueryLength ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 ## Merge all overlapping Path instances in a list without considering the identifiers |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 # Start by sorting the Path instances by their increasing min coordinate |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 # @return: a new list with the merged Path instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 def mergePathsInList( lPaths ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
711 lMergedPaths = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 if len(lPaths)==0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 return lMergedPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 lSortedPaths = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 prev_count = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 for iPath in lSortedPaths[0:]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 if prev_count != len(lSortedPaths): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 for i in lSortedPaths[ prev_count + 1: ]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 if iPath.isOverlapping( i ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 iPath.merge( i ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 isAlreadyInList = False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 for newPath in lMergedPaths: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 if newPath.isOverlapping( iPath ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 isAlreadyInList = True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 newPath.merge( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 lMergedPaths [ lMergedPaths.index( newPath ) ] = newPath |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 if not isAlreadyInList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 lMergedPaths.append( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 prev_count += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 return lMergedPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 mergePathsInList = staticmethod( mergePathsInList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 ## Merge all overlapping Path instances in a list without considering if subjects are overlapping. |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 # Start by sorting the Path instances by their increasing min coordinate. |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
739 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
740 # @return: a new list with the merged Path instances |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 def mergePathsInListUsingQueryCoordsOnly( lPaths ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 lMergedPaths = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 if len(lPaths)==0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 return lMergedPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 lSortedPaths = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 prev_count = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 for iPath in lSortedPaths[0:]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 if prev_count != len(lSortedPaths): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 for i in lSortedPaths[ prev_count + 1: ]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 if iPath.isQueryOverlapping( i ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 iPath.merge( i ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 isAlreadyInList = False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 for newPath in lMergedPaths: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 if newPath.isQueryOverlapping( iPath ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 isAlreadyInList = True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 newPath.merge( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 lMergedPaths [ lMergedPaths.index( newPath ) ] = newPath |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 if not isAlreadyInList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 lMergedPaths.append( iPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 prev_count += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 return lMergedPaths |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 mergePathsInListUsingQueryCoordsOnly = staticmethod( mergePathsInListUsingQueryCoordsOnly ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 ## Convert a Path file into a GFF file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 # @param pathFile: name of the input Path file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 # @param gffFile: name of the output GFF file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 # @param source: source to write in the GFF file (column 2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 # @note the 'path' query is supposed to correspond to the 'gff' first column |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 def convertPathFileIntoGffFile( pathFile, gffFile, source="REPET", verbose=0 ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 dId2PathList = PathUtils.getDictOfListsWithIdAsKeyFromFile( pathFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 if verbose > 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 msg = "number of chains: %i" % ( len(dId2PathList.keys()) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 sys.stdout.write( "%s\n" % msg ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 sys.stdout.flush() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 gffFileHandler = open( gffFile, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 for id in dId2PathList.keys(): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 if len( dId2PathList[ id ] ) == 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 iPath = dId2PathList[ id ][0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 string = iPath.toStringAsGff( ID="%i" % iPath.getIdentifier(), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 source=source ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 gffFileHandler.write( "%s\n" % string ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 iPathrange = PathUtils.convertPathListToPathrange( dId2PathList[ id ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 string = iPathrange.toStringAsGff( ID="ms%i" % iPathrange.getIdentifier(), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 source=source ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 gffFileHandler.write( "%s\n" % string ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 count = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 for iPath in dId2PathList[ id ]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 count += 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 string = iPath.toStringAsGff( type="match_part", |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
799 ID="mp%i-%i" % ( iPath.getIdentifier(), count ), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 Parent="ms%i" % iPathrange.getIdentifier(), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 source=source ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 gffFileHandler.write( "%s\n" % string ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 gffFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 convertPathFileIntoGffFile = staticmethod( convertPathFileIntoGffFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
808 ## Convert a Path file into a Set file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 # replace old parser.pathrange2set |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 # @param pathFile: name of the input Path file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 # @param setFile: name of the output Set file |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
812 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 def convertPathFileIntoSetFile( pathFile, setFile ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 pathFileHandler = open( pathFile, "r" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 setFileHandler = open( setFile, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 iPath = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 while True: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 line = pathFileHandler.readline() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 if line == "": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 break |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 iPath.setFromString( line ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 iSet = iPath.getSubjectAsSetOfQuery() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 iSet.write( setFileHandler ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 pathFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 setFileHandler.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 convertPathFileIntoSetFile = staticmethod( convertPathFileIntoSetFile ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 ## Write Path File without duplicated Path (same query, same subject and same coordinate) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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831 # @param inputFile: name of the input Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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832 # @param outputFile: name of the output Path file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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833 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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834 def removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName(inputFile, outputFile): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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835 f = open(inputFile, "r") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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836 line = f.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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837 previousQuery = "" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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838 previousSubject = "" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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839 lPaths = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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840 while line: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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841 iPath = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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842 iPath.setFromString(line) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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843 query = iPath.getQueryName() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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844 subject = iPath.getSubjectName() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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845 if (query != previousQuery or subject != previousSubject) and lPaths != []: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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846 lPathsWithoutDuplicate = PathUtils.getPathListWithoutDuplicatesOnQueryCoord(lPaths) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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847 PathUtils.writeListInFile(lPathsWithoutDuplicate, outputFile, "a") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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848 lPaths = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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849 lPaths.append(iPath) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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850 previousQuery = query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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851 previousSubject = subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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852 line = f.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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853 lPathsWithoutDuplicate = PathUtils.getPathListWithoutDuplicatesOnQueryCoord(lPaths) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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854 PathUtils.writeListInFile(lPathsWithoutDuplicate, outputFile, "a") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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855 f.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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856 removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName = staticmethod(removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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857 |
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858 |