Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/sql/test/Test_TableSeqAdaptator.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed 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)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 unittest
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33 import os
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34 import time
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35 from commons.core.sql.DbMySql import DbMySql
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36 from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
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37 from commons.core.seq.Bioseq import Bioseq
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38 from commons.core.coord.Set import Set
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39 from commons.core.utils.FileUtils import FileUtils
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40
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41
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42 class Test_TableSeqAdaptator( unittest.TestCase ):
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43
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44 def setUp( self ):
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45 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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46 self.fileUtils = FileUtils()
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47 self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
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48 configF = open(self._configFileName, "w" )
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49 configF.write( "[repet_env]\n" )
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50 configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
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51 configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
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52 configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
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53 configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
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54 configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
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55 configF.close()
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56 self._db = DbMySql( cfgFileName=self._configFileName )
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57 self._table = "dummySeqTable_%s" % ( self._uniqId )
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58 self._tsA = TableSeqAdaptator( self._db, self._table )
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59
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60
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61 def tearDown( self ):
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62 self._db.dropTable( self._table )
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63 self._db.close()
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64 os.remove( self._configFileName )
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65 self._configFileName = ""
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66
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67
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68 ##################################################################################
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69 ################## Tests for methods in ITableSeqAdaptator #######################
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70 ##################################################################################
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71
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72 def test_insert( self ):
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73 bs = Bioseq( "seq1", "AGCGATGACGATGCGAGT" )
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74 self._db.createTable( self._table, "fasta" )
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75 self._tsA.insert( bs )
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76
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77 expBioseqTuple = (("seq1", "AGCGATGACGATGCGAGT", "seq1", 18L), )
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78
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79 sqlCmd = "SELECT * FROM %s" % ( self._table )
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80 self._db.execute( sqlCmd )
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81 obsBioseqTuple = self._db.cursor.fetchall()
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82
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83 self.assertEqual( expBioseqTuple, obsBioseqTuple )
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84
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85
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86 def test_insertList( self ):
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87 bs1 = Bioseq( "seq1 desc", "AGCGATGACGATGCGAGT" )
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88 bs2 = Bioseq( "seq2", "AGCGATGACGATGCGAGT")
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89 bs3 = Bioseq( "seq3", "GCGATGCAGATGACGGCGGATGC")
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90 lBioseq = [ bs1, bs2, bs3 ]
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91 self._db.createTable( self._table, "fasta" )
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92 self._tsA.insertList( lBioseq )
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93
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94 tuple1 = ("seq1", "AGCGATGACGATGCGAGT", "seq1 desc", 18L)
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95 tuple2 = ("seq2", "AGCGATGACGATGCGAGT", "seq2", 18L)
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96 tuple3 = ("seq3", "GCGATGCAGATGACGGCGGATGC", "seq3", 23L)
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97 expBioseqTuple = ( tuple1, tuple2, tuple3 )
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98
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99 sqlCmd = "SELECT * FROM %s" % ( self._table )
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100 self._db.execute( sqlCmd )
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101 obsBioseqTuple = self._db.cursor.fetchall()
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102
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103 self.assertEquals(expBioseqTuple, obsBioseqTuple)
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104
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105
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106 def test_getAccessionsList(self):
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107 faFileName = "dummyFaFile_%s" % ( self._uniqId )
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108 faF = open( faFileName, "w" )
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109 faF.write(">seq1\n")
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110 faF.write("AGCGATGACGATGCGAGT\n")
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111 faF.write(">seq2\n")
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112 faF.write("GCGATGCAGATGACGGCGGATGC\n")
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113 faF.close()
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114 self._db.createTable( self._table, "fasta", faFileName )
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115 lExp = [ "seq1", "seq2" ]
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116 lExp.sort()
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117 lObs = self._tsA.getAccessionsList()
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118 lObs.sort()
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119 self.assertEqual( lObs, lExp )
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120 os.remove( faFileName )
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121
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122
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123 def test_saveAccessionsListInFastaFile(self):
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124 expFileName = "dummyFaFile_%s" % ( self._uniqId )
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125 expF = open( expFileName, "w" )
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126 expF.write(">seq1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
127 expF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
128 expF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
129 expF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
130 expF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
131 self._db.createTable( self._table, "fasta", expFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
132 lAccessions = [ "seq1", "seq2" ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
133 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
134 self._tsA.saveAccessionsListInFastaFile( lAccessions, obsFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
135 self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
136 os.remove( expFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
137 os.remove( obsFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
138
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
139 def test_exportInFastaFile(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
140 expFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
141 faF = open( expFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
142 faF.write(">seq1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
143 faF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
144 faF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
145 faF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
146 faF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
147 self._db.createTable( self._table, "fasta", expFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
148 obsFileName = "dummyFaFileObs_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
149 self._tsA.exportInFastaFile( obsFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
150 self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
151 os.remove( expFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
152 os.remove( obsFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
153
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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154 ##################################################################################
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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155 ########################### Tests for other methods ##############################
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
156 ##################################################################################
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
157
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
158 def test_insertWithBioseqEmpty( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
159 bs = Bioseq( "", "" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
160 self._db.createTable( self._table, "fasta" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
161 exp = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
162 obs = self._tsA.insert(bs)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
163 self.assertEqual( exp, obs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
164
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
165
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
166 def test_getBioseqFromHeader( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
167 faFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
168 faF = open( faFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
169 faF.write(">seq1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
170 faF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
171 faF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
172 faF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
173 faF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
174 self._db.createTable( self._table, "fasta", faFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
175 exp = Bioseq( "seq1", "AGCGATGACGATGCGAGT" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
176 obs = self._tsA.getBioseqFromHeader( "seq1" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
177 self.assertEqual( obs, exp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
178 exp = Bioseq( "seq2", "GCGATGCAGATGACGGCGGATGC" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
179 obs = self._tsA.getBioseqFromHeader( "seq2" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
180 self.assertEqual( obs, exp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
181 os.remove( faFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
182
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
183
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
184 def test_getSeqLengthFromAccession( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
185 inFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
186 inF = open( inFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
187 inF.write(">seq1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
188 inF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
189 inF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
190 inF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
191 inF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
192 self._db.createTable( self._table, "fasta", inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
193 exp = 18
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
194 obs = self._tsA.getSeqLengthFromAccession( "seq1" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
195 self.assertEqual( obs, exp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
196 os.remove( inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
197
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
198
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
199 def test_getSeqLengthFromDescription( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
200 inFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
201 inF = open( inFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
202 inF.write(">seq1 descriptionfield\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
203 inF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
204 inF.write(">seq2 descriptionfield\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
205 inF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
206 inF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
207 self._db.createTable( self._table, "fasta", inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
208 exp = 18
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
209 obs = self._tsA.getSeqLengthFromDescription( "seq1 descriptionfield" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
210 self.assertEqual( obs, exp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
211 os.remove( inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
212
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
213
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
214 def test_getAccessionAndLengthList( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
215 inFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 inF = open( inFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
217 inF.write(">seq1\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
218 inF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
219 inF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 inF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221 inF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
222 self._db.createTable( self._table, "fasta", inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
223 lSeq1 = ("seq1", 18)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 lSeq2 = ("seq2", 23)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
225 lExp = [lSeq1,lSeq2]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
226 lObs = self._tsA.getAccessionAndLengthList()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
227 self.assertEqual( lObs, lExp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228 os.remove( inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
230
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231 def test_getSeqLengthFromAccessionWithSingleQuote( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232 inFileName = "dummyFaFile_%s" % ( self._uniqId )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
233 inF = open( inFileName, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
234 inF.write(">seq1'\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235 inF.write("AGCGATGACGATGCGAGT\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236 inF.write(">seq2\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
237 inF.write("GCGATGCAGATGACGGCGGATGC\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
238 inF.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 self._db.createTable( self._table, "fasta", inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
240 exp = 18
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241 obs = self._tsA.getSeqLengthFromAccession( "seq1'" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
242 self.assertEqual( obs, exp )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
243 os.remove( inFileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
244
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
245
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 def test_getSubSequence_directStrand( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 self._db.createTable( self._table, "seq" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248 chr = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249 chr.setHeader( "chr2" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
251 self._tsA.insert( chr )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
252 exp = "TTTGGG"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
253 obs = self._tsA.getSubSequence( "chr2", 13, 18 )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
254 self.assertEqual( exp, obs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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255
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256
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257 def test_getSubSequence_reverseStrand( self ):
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258 self._db.createTable( self._table, "seq" )
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259 chr = Bioseq()
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260 chr.setHeader( "chr2" )
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261 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
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262 self._tsA.insert( chr )
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263 exp = "CCCAAA"
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264 obs = self._tsA.getSubSequence( "chr2", 18, 13 )
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265 self.assertEqual( exp, obs )
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266
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267
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268 def test_getBioseqFromSetList_directStrand( self ):
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269 self._db.createTable( self._table, "seq" )
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270 chr = Bioseq()
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271 chr.setHeader( "chr2" )
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272 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
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273 self._tsA.insert( chr )
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274 lSets = []
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275 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 1, 10 ) )
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276 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 16, 25 ) )
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277 exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 1..10,16..25", "AAAAAAAAAAGGGGGGGGGG" )
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278 obs = self._tsA.getBioseqFromSetList( lSets )
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279 self.assertEqual( exp, obs )
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280
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281
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282 def test_getBioseqFromSetList_reverseStrand( self ):
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283 self._db.createTable( self._table, "seq" )
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284 chr = Bioseq()
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285 chr.setHeader( "chr2" )
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286 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
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287 self._tsA.insert( chr )
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288 lSets = []
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289 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 10, 1 ) )
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290 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 25, 16 ) )
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291 exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 25..16,10..1", "CCCCCCCCCCTTTTTTTTTT" )
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292 obs = self._tsA.getBioseqFromSetList( lSets )
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293 self.assertEqual( exp, obs )
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294
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295
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296 def test_isAccessionInTable_true( self ):
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297 self._db.createTable( self._table, "seq" )
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298 chr = Bioseq()
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299 chr.setHeader( "chr2" )
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300 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
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301 self._tsA.insert( chr )
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302
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303 obs = self._tsA.isAccessionInTable( "chr2" )
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304 self.assertTrue( obs )
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305
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306
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307 def test_isAccessionInTable_false( self ):
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308 self._db.createTable( self._table, "seq" )
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309 chr = Bioseq()
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310 chr.setHeader( "chr2" )
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311 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
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312 self._tsA.insert( chr )
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313
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314 obs = self._tsA.isAccessionInTable( "chr1" )
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315 self.assertFalse( obs )
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316
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317
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318 test_suite = unittest.TestSuite()
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319 test_suite.addTest( unittest.makeSuite( Test_TableSeqAdaptator ) )
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320 if __name__ == "__main__":
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321 unittest.TextTestRunner(verbosity=2).run( test_suite )