Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/ITablePathAdaptator.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 ## Interface for TablePathAdaptator |
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33 # |
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34 class ITablePathAdaptator (object): |
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35 |
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36 ## Give the data contained in the table as a list of Path instances |
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37 # |
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38 # @return lPaths list of path instances |
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39 # |
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40 def getListOfAllPaths( self ): |
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41 pass |
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42 |
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43 ## Give a list of Path instances having the same identifier |
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44 # |
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45 # @param id integer identifier number |
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46 # @return lPath a list of Path instances |
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47 # |
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48 # @warning old name was getPathList_from_num |
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49 # |
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50 def getPathListFromId( self, id ): |
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51 pass |
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52 |
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53 ## Give a list of Path instances according to the given list of identifier numbers |
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54 # |
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55 # @param lId integer list |
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56 # @return lPath a list of Path instances |
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57 # |
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58 # @warning old name was getPathList_from_numlist |
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59 # |
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60 def getPathListFromIdList( self, lId ): |
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61 pass |
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62 |
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63 ## Give a list of Path instances having the same given query name |
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64 # |
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65 # @param query string name of the query |
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66 # @return lPath a list of Path instances |
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67 # |
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68 # @warning old name was getPathList_from_query |
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69 # |
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70 def getPathListFromQuery( self, query ): |
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71 pass |
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72 |
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73 ## Give a list with all the distinct identifiers corresponding to the query |
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74 # |
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75 # @param query string name of the query |
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76 # @return lId a list of integer |
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77 # |
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78 # @warning old name was getPathList_from_query |
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79 # |
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80 def getIdListFromQuery( self, query ): |
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81 pass |
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82 |
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83 ## Give a list with all the distinct identifiers corresponding to the subject |
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84 # |
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85 # @param subject string name of the subject |
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86 # @return lId a list of integer |
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87 # |
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88 # @warning old name was getPathList_from_subject |
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89 # |
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90 def getIdListFromSubject( self, subject ): |
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91 pass |
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92 |
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93 ## Insert a path instance |
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94 # |
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95 # @param obj a path instance |
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96 # @param delayed boolean indicating if the insert must be delayed |
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97 # |
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98 # @note data are inserted such that the query is always on the direct strand |
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99 # |
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100 # @warning old name was insAPath |
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101 # |
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102 def insert(self, obj, delayed = False): |
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103 pass |
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104 |
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105 ## Insert a list of Path instances |
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106 # |
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107 # @param l a list of Path instances |
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108 # @param delayed boolean |
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109 # |
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110 # @warning old name was insPathList |
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111 # |
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112 def insertList(self, l, delayed = False): |
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113 pass |
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114 |
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115 ## Give a list of the identifier number contained in the table |
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116 # |
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117 # @return l integer list |
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118 # |
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119 # @warning old name was getPath_num |
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120 # |
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121 def getIdList(self): |
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122 pass |
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123 |
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124 ## Give a list of Path instances having the same given subject name |
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125 # |
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126 # @param subject string name of the subject |
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127 # @return lPath a list of Path instances |
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128 # |
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129 # @warning old name was getPath_num |
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130 # |
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131 def getPathListFromSubject( self, subject ): |
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132 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 |
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134 ## Give a list of the distinct subject names present in the table |
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135 # |
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136 # @return lDistinctTypeNames string list |
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137 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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138 # @warning old name was getListDistinctSubjectName |
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139 # |
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140 def getSubjectList(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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141 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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142 |
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143 ## Give a list of the distinct query names present in the table |
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144 # |
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145 # @return lDistinctQueryNames string list |
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146 # |
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147 # @warning old name was getListDistinctQueryName |
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148 # |
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149 def getQueryList(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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150 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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151 |
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152 ## Give a list of Set instance list from the path contained on a query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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153 # |
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154 # @param queryName string query name |
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155 # @return lSet list of set instance |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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156 # |
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157 def getSubjectListFromQuery (self, queryName): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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158 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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159 |
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160 ## Give a list of Path instances with the given query and subject, both on direct strand |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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161 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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162 # @param query string query name |
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163 # @param subject string subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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164 # @return 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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165 # |
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166 # @warning old name was getListPathsWithDirectQueryDirectSubjectPerQuerySubject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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167 # |
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168 def getPathListWithDirectQueryDirectSubjectFromQuerySubject( self, query, subject ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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169 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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170 |
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171 ## Give a list of Path instances with the given query on direct strand and the given subject on reverse strand |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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172 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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173 # @param query string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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174 # @param subject string subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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175 # @return 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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176 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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177 # @warning old name was getListPathsWithDirectQueryReverseSubjectPerQuerySubject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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178 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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179 def getPathListWithDirectQueryReverseSubjectFromQuerySubject( self, query, subject ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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180 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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181 |
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182 ## Give the number of Path instances with the given query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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183 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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184 # @param query string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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185 # @return pathNb integer the number of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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186 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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187 # @warning old name was getNbPaths_from_query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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188 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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189 def getNbPathsFromQuery( self, query ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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190 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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191 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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192 ## Give the number of Path instances with the given subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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193 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 # @param subject string subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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195 # @return pathNb integer the number of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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196 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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197 # @warning old name was getNbPaths_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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198 # |
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199 def getNbPathsFromSubject( self, subject ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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201 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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202 ## Give the number of distinct path identifiers |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 # @return idNb integer the number of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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205 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 # @warning old name was getNbAllPathsnums |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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208 def getNbIds( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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209 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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211 ## Give the number of distinct path identifiers for a given subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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212 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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213 # subjectName string subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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214 # @return idNb integer the number of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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215 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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216 # @warning old name was getNbPathsnums_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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217 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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218 def getNbIdsFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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219 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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221 ## Give the number of distinct path identifiers for a given query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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222 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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223 # @param queryName string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 # @return idNb integer the number of Path instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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225 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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226 # @warning old name was getNbPathsnums_from_query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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227 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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228 def getNbIdsFromQuery( self, queryName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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229 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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230 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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231 ## Give a list of Path instances overlapping a given region |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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232 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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233 # @param query string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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234 # @param start integer start coordinate |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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235 # @param end integer end coordinate |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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236 # @return lPath 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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237 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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238 def getPathListOverlappingQueryCoord( self, query, start, end ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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239 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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241 ## Give a list of Set instances overlapping a given region |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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242 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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243 # @param query string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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244 # @param start integer start coordinate |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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245 # @param end integer end coordinate |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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246 # @return lSet list of Set instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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247 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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248 # @warning old name was getSetList_from_qcoord |
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249 # |
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250 def getSetListOverlappingQueryCoord(self, query, start, end): |
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251 pass |
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252 |
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253 ## Give a list of Path instances included in a given query region |
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254 # |
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255 # @param query string query name |
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256 # @param start integer start coordinate |
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257 # @param end integer end coordinate |
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258 # @return lPaths list of Path instances |
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259 # |
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260 # @warning old name was getIncludedPathList_from_qcoord |
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261 # |
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262 def getPathListIncludedInQueryCoord( self, query, start, end ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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263 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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264 |
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265 ## Give a list of Set instances included in a given region |
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266 # |
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267 # @param query string query name |
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268 # @param start integer start coordinate |
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269 # @param end integer end coordinate |
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270 # @return lSet list of Set instances |
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271 # |
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272 # @warning old name was getInSetList_from_qcoord |
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273 # |
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274 def getSetListIncludedInQueryCoord(self, query, start, end): |
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275 pass |
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276 |
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277 ## Give a a list of Path instances sorted by query coordinates |
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278 # |
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279 # @return lPaths list of Path instances |
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280 # |
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281 # @warning old name was getListOfPathsSortedByQueryCoord |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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282 # |
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283 def getPathListSortedByQueryCoord( self ): |
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284 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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285 |
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286 ## Give a a list of Path instances sorted by query coordinates for a given query |
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287 # |
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288 # @param queryName string query name |
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289 # @return 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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290 # |
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291 def getPathListSortedByQueryCoordFromQuery( self, queryName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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293 |
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294 ## Give a list of path instances sorted by increasing E-value |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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295 # |
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296 # queryName string query name |
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297 # @return 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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298 # |
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299 def getPathListSortedByIncreasingEvalueFromQuery( self, queryName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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300 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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301 |
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302 ## Give a cumulative length of all paths (fragments) for a given subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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303 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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304 # @param subjectName string subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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305 # @return nb Cumulative length for all path |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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306 # @warning doesn't take into account the overlaps !! |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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307 # @warning old name was getCumulPathLength_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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308 # |
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309 def getCumulLengthFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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311 |
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312 ## Give a list of the length of all chains of paths for a given subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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313 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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314 # @param subjectName string name of the subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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315 # @return lChainLengths list of lengths per chain of paths |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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316 # @warning doesn't take into account the overlaps !! |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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317 # @warning old name was getListChainLength_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319 def getChainLengthListFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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322 ## Give a list of identity of all chains of paths for a given subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 # @param subjectName string name of the subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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325 # @return lChainIdentities list of identities per chain of paths |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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326 # @warning doesn't take into account the overlaps !! |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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327 # @warning old name was getListChainIdentity_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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328 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 def getChainIdentityListFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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330 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 ## Give a list of Path lists sorted by weighted identity. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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333 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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334 # @param qry query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 # @return lChains list of chains |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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336 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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337 def getListOfChainsSortedByAscIdentityFromQuery( self, qry ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 ## Give a list of the length of all paths for a given subject name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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341 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 # @param subjectName string name of the subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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343 # @return lPathLengths list of lengths per path |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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344 # @warning doesn't take into account the overlaps !! |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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345 # @warning old name was getListPathLength_from_subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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346 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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347 def getPathLengthListFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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348 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 ## Give a a list with all distinct identifiers for a given subject sorted in decreasing order according to the length of the chains |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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352 # @return lPathNums a list of paths Id |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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353 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 # @warning old name was getPathNumListSortedByDecreasingChainLengthFromSubject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 def getIdListSortedByDecreasingChainLengthFromSubject( self, subjectName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 pass |
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 ## Give a list of Set instance list from the path contained on a query name |
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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 query string query name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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362 # @return lSet list of set instance |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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363 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 # @warning old name was getSetList_from_contig |
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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366 def getSetListFromQuery(self, query): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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367 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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368 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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369 ## Delete path corresponding to a given identifier number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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370 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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371 # @param id integer identifier number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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372 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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373 # @warning old name was delPath_from_num |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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374 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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375 def deleteFromId(self,id): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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376 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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377 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 ## Delete path corresponding to a given list of identifier number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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379 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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380 # @param lId list of identifier number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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382 # @warning old name was delPath_from_numlist |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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383 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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384 def deleteFromIdList(self,lId): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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385 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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386 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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387 ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 # @param id1 integer path number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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390 # @param id2 integer path number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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391 # @return newId integer id used to join |
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 # @warning old name was joinPath |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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394 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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395 def joinTwoPaths(self,id1,id2): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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398 ## Get a new id number |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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399 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 # @return newId integer new id |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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401 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 def getNewId(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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404 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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405 ## Test if table is empty |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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407 def isEmpty( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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409 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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410 ## Create a 'pathRange' table from a 'path' table. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 # The output table summarizes the information per identifier. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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412 # The min and max value are taken. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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413 # The identity is averaged over the fragments. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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414 # It may overwrite an existing table. |
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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 # @param outTable string name of the output table |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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417 # @return outTable string Table which summarizes the information per identifier |
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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 def path2PathRange( self, outTable="" ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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420 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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421 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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422 ## Return the number of times a given instance is present in the table |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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423 # The identifier is not considered, |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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424 # only coordinates, score, E-value and identity. |
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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.
yufei-luo
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426 # @return nbOcc integer |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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427 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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428 def getNbOccurrences( self, iPath ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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429 pass |