Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/ITableMapAdaptator.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 TableMapAdaptator |
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33 # |
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34 class ITableMapAdaptator(object): |
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35 |
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36 ## Insert a map instance |
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37 # |
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38 # @param obj map or set |
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39 # @param delayed boolean must the insert be delayed |
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40 # |
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41 # @warning old name was insAMap |
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42 # |
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43 def insert(self, obj, delayed=False): |
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44 pass |
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45 |
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46 |
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47 ## Insert a list of Map or Set or Match instances |
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48 # |
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49 # @param l a list of object instances |
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50 # @param delayed boolean |
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51 # |
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52 # @warning old name was insMapList |
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53 # |
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54 def insertList(self, l, delayed = False): |
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55 pass |
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56 |
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57 ## Give a list of the distinct seqName/chr present in the table |
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58 # |
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59 # @return lDistinctContigNames string list |
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60 # |
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61 # @warning old name was getContig_name |
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62 # |
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63 def getSeqNameList(self): |
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64 pass |
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65 |
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66 |
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67 ## Give a list of Map instances having a given seq name |
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68 # |
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69 # @param seqName string seq name |
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70 # @return lMap list of instances |
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71 # |
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72 # @warning old name was get_MapList_from_contig |
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73 # |
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74 def getMapListFromSeqName(self, seqName): |
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75 pass |
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76 |
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77 |
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78 ## Return a list of Set instances from a given sequence name |
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79 # |
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80 # @param seqName string sequence name |
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81 # @return lSets list of Set instances |
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82 # |
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83 # @warning old name was getSetList_from_contig |
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84 # |
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85 def getSetListFromSeqName( self, seqName ): |
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86 pass |
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87 |
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88 |
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89 ## Give a map instances list overlapping a given region |
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90 # |
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91 # @param seqName string seq name |
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92 # @param start integer start coordinate |
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93 # @param end integer end coordinate |
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94 # @return lMap list of map instances |
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95 # |
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96 # @warning old name was getMapList_from_qcoord |
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97 # |
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98 def getMapListOverlappingCoord(self, seqName, start, end): |
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99 pass |
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100 |
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101 |
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102 ## Return a list of Set instances overlapping a given region |
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103 # |
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104 # @param seqName string sequence name |
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105 # @param start integer start coordinate |
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106 # @param end integer end coordinate |
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107 # @return lSet list of Set instances |
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108 # |
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109 # @warning old name was getSetList_from_qcoord |
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110 # |
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111 def getSetListOverlappingCoord( self, seqName, start, end ): |
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112 pass |
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113 |