Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/TableMatchAdaptator.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 from commons.core.sql.TableAdaptator import TableAdaptator |
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33 from commons.core.sql.ITableMatchAdaptator import ITableMatchAdaptator |
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34 from commons.core.coord.Match import Match |
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35 |
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36 ## Adaptator for Match table |
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37 # |
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38 class TableMatchAdaptator( TableAdaptator, ITableMatchAdaptator ): |
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39 |
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40 ## Give a list of Match instances given a query name |
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41 # |
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42 # @param query string sequence name |
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43 # @return lMatches list of Match instances |
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44 # |
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45 def getMatchListFromQuery( self, query ): |
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46 sqlCmd = "SELECT * FROM %s WHERE query_name='%s';" % ( self._table, query ) |
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47 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) |
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48 |
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49 ## Give a list of Match instances having the same identifier |
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50 # |
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51 # @param id integer identifier number |
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52 # @return lMatch a list of Match instances |
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53 # |
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54 def getMatchListFromId( self, id ): |
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55 sqlCmd = "SELECT * FROM %s WHERE path='%d';" % ( self._table, id ) |
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56 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) |
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57 return lMatch |
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58 |
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59 ## Give a list of Match instances according to the given list of identifier numbers |
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60 # |
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61 # @param lId integer list |
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62 # @return lMatch a list of Match instances |
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63 # |
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64 def getMatchListFromIdList( self, lId ): |
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65 lMatch=[] |
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66 if lId == []: |
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67 return lMatch |
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68 sqlCmd = "select * from %s where path=%d" % (self._table, lId[0]) |
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69 for i in lId[1:]: |
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70 sqlCmd += " or path=%d" % (i) |
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71 sqlCmd += ";" |
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72 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) |
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73 return lMatch |
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74 |
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75 ## Give the data contained in the table as a list of Match instances |
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76 # |
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77 # @return lMatchs list of match instances |
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78 # |
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79 def getListOfAllMatches( self ): |
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80 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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81 lMatches = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) |
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82 return lMatches |
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83 |
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84 def _getInstanceToAdapt(self): |
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85 iMatch = Match() |
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86 return iMatch |
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87 |
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88 def _getTypeAndAttr2Insert(self, match): |
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89 type2Insert = ("'%s'","'%d'","'%d'","'%d'","'%f'","'%f'","'%s'","'%d'","'%d'","'%d'","'%f'","'%g'","'%d'","'%f'","'%d'") |
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90 attr2Insert = ( match.range_query.seqname, match.range_query.start, \ |
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91 match.range_query.end, match.query_length, match.query_length_perc, \ |
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92 match.match_length_perc, match.range_subject.seqname, match.range_subject.start,\ |
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93 match.range_subject.end, match.subject_length, match.subject_length_perc, \ |
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94 match.e_value, match.score, match.identity, \ |
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95 match.id) |
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96 return type2Insert, attr2Insert |
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97 |
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98 def _escapeAntislash(self, obj): |
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99 obj.range_query.seqname = obj.range_query.seqname.replace("\\", "\\\\") |
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100 obj.range_subject.seqname = obj.range_subject.seqname.replace("\\", "\\\\") |