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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import unittest
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33 import os
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34 import time
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35 from commons.core.utils.FileUtils import FileUtils
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36 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
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37
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38
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39 class Test_ChangeSequenceHeaders( unittest.TestCase ):
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40
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41 def setUp( self ):
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42 self._i = ChangeSequenceHeaders()
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43 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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44
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45
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46 def tearDown( self ):
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47 self._i = None
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48 self._uniqId = None
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49
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50
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51 def test_script_no_input_file( self ):
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52 cDir = os.getcwd()
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53
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54 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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55
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56 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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57
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58 cmd = "python ../ChangeSequenceHeaders.py"
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59 cmd += " -i %s" % ( inFile )
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60 cmd += " -f fasta"
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61 cmd += " -s 1"
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62 cmd += " -p TE"
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63 cmd += " -o %s" % ( obsFile )
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64 exitStatus = os.system( cmd )
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65
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66 self.assertFalse( exitStatus == 0 )
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67
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68 os.chdir( cDir )
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69
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70
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71 def test_shortenSequenceHeadersForFastaFile_fasta_script( self ):
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72 cDir = os.getcwd()
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73
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74 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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75 inF = open( inFile, "w" )
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76 inF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" )
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77 inF.write( ">consensus524\nGTGCGGATGGAACAGT\n" )
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78 inF.close()
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79
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80 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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81
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82 expFile = "dummyExpFile_%s" % ( self._uniqId )
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83 expF = open( expFile, "w" )
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84 expF.write( ">TE1\nATGTACGATGACGATCAG\n" )
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85 expF.write( ">TE2\nGTGCGGATGGAACAGT\n" )
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86 expF.close()
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87
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88 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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89
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90 cmd = "python ../ChangeSequenceHeaders.py"
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91 cmd += " -i %s" % ( inFile )
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92 cmd += " -f fasta"
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93 cmd += " -s 1"
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94 cmd += " -p TE"
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95 cmd += " -l %s" % ( linkFile )
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96 cmd += " -o %s" % ( obsFile )
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97 exitStatus = os.system( cmd )
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98
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99 self.assertTrue( exitStatus == 0 )
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100 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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101
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102 for f in [ inFile, linkFile, expFile, obsFile ]:
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103 os.remove( f )
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104 os.chdir( cDir )
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105
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106
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107 def test_retrieveInitialSequenceHeaders_fasta_script( self ):
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108 cDir = os.getcwd()
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109
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110 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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111 inF = open( inFile, "w" )
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112 inF.write( ">seq2\nATGTACGATGACGATCAG\n" )
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113 inF.write( ">seq1\nGTGCGGATGGAACAGT\n" )
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114 inF.close()
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115
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116 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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117 linkF = open( linkFile, "w" )
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118 linkF.write( "seq1\tconsensus524\t1\t18\n" )
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119 linkF.write( "seq2\tDmelChr4-B-G387-MAP16\t1\t16\n" )
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120 linkF.write( "seq3\treference2\n" )
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121 linkF.close()
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122
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123 expFile = "dummyExpFile_%s" % ( self._uniqId )
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124 expF = open( expFile, "w" )
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125 expF.write( ">DmelChr4-B-G387-MAP16\nATGTACGATGACGATCAG\n" )
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126 expF.write( ">consensus524\nGTGCGGATGGAACAGT\n" )
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127 expF.close()
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128
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129 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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130
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131 cmd = "python ../ChangeSequenceHeaders.py"
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132 cmd += " -i %s" % ( inFile )
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133 cmd += " -f fasta"
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134 cmd += " -s 2"
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135 cmd += " -l %s" % ( linkFile )
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136 cmd += " -o %s" % ( obsFile )
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137 exitStatus = os.system( cmd )
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138
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139 self.assertTrue( exitStatus == 0 )
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140 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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141
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142 for f in [ inFile, linkFile, expFile, obsFile ]:
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143 os.remove( f )
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144 os.chdir( cDir )
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145
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146 def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_Blastclust( self ):
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147 cDir = os.getcwd()
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148
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149 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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150 inF = open( inFile, "w" )
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151 inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
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152 inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
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153 inF.close()
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154
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155 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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156 linkF = open( linkFile, "w" )
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157 linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" )
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158 linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" )
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159 linkF.write( "seq3\treference2\n" )
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160 linkF.close()
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161
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162 expFile = "dummyExpFile_%s" % ( self._uniqId )
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163 expF = open( expFile, "w" )
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164 expF.write( ">BlastclustCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" )
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165 expF.write( ">BlastclustCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" )
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166 expF.close()
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167
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168 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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169
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170 whichCluster = "A"
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171 cmd = "python ../ChangeSequenceHeaders.py"
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172 cmd += " -i %s" % ( inFile )
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173 cmd += " -f fasta"
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174 cmd += " -s 2"
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175 cmd += " -l %s" % ( linkFile )
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176 cmd += " -w %s" % ( whichCluster )
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177 cmd += " -o %s" % ( obsFile )
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178 exitStatus = os.system( cmd )
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179
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180 self.assertTrue( exitStatus == 0 )
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181 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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182
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183 for f in [ inFile, linkFile, expFile, obsFile ]:
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184 os.remove( f )
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185 os.chdir( cDir )
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186
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187 def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_Blastclust( self ):
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188 cDir = os.getcwd()
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189
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190 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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191 inF = open( inFile, "w" )
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192 inF.write( ">BlastclustCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
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193 inF.write( ">BlastclustCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
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194 inF.close()
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195
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196 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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197 linkF = open( linkFile, "w" )
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198 linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" )
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199 linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" )
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200 linkF.write( "seq3\treference2\n" )
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201 linkF.close()
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202
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203 expFile = "dummyExpFile_%s" % ( self._uniqId )
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204 expF = open( expFile, "w" )
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205 expF.write( ">DHX-incomp_Blc8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" )
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206 expF.write( ">RLX-incomp_Blc1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" )
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207 expF.close()
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208
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209 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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210
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211 whichCluster = "B"
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212 cmd = "python ../ChangeSequenceHeaders.py"
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213 cmd += " -i %s" % ( inFile )
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214 cmd += " -f fasta"
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215 cmd += " -s 2"
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216 cmd += " -l %s" % ( linkFile )
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217 cmd += " -w %s" % ( whichCluster )
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218 cmd += " -o %s" % ( obsFile )
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219 exitStatus = os.system( cmd )
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220
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221 self.assertTrue( exitStatus == 0 )
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222 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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223
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224 for f in [ inFile, linkFile, expFile, obsFile ]:
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225 os.remove( f )
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226 os.chdir( cDir )
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227
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228 def test_retrieveInitialSequenceHeaders_fastaFromClustering_afterLTRHarvest_MCL( self ):
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229 cDir = os.getcwd()
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230
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231 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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232 inF = open( inFile, "w" )
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233 inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
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234 inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
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235 inF.close()
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236
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237 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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238 linkF = open( linkFile, "w" )
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239 linkF.write( "seq1\tchunk1 (dbseq-nr 1) [41806,41825]\t1\t18\n" )
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240 linkF.write( "seq2\tchunk2 (dbseq-nr 6) [41006,41023]\t1\t16\n" )
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241 linkF.write( "seq3\treference2\n" )
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242 linkF.close()
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243
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244 expFile = "dummyExpFile_%s" % ( self._uniqId )
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245 expF = open( expFile, "w" )
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246 expF.write( ">MCLCluster1Mb3_chunk2 (dbseq-nr 6) [41006,41023]\nATGTACGATGACGATCAG\n" )
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247 expF.write( ">MCLCluster8Mb4_chunk1 (dbseq-nr 1) [41806,41825]\nGTGCGGATGGAACAGT\n" )
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248 expF.close()
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249
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250 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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251
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252 whichCluster = "A"
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253 cmd = "python ../ChangeSequenceHeaders.py"
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254 cmd += " -i %s" % ( inFile )
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255 cmd += " -f fasta"
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256 cmd += " -s 2"
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257 cmd += " -l %s" % ( linkFile )
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258 cmd += " -w %s" % ( whichCluster )
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259 cmd += " -o %s" % ( obsFile )
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260 exitStatus = os.system( cmd )
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261
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262 self.assertTrue( exitStatus == 0 )
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263 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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264
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265 for f in [ inFile, linkFile, expFile, obsFile ]:
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266 os.remove( f )
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267 os.chdir( cDir )
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268
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269 def test_retrieveInitialSequenceHeaders_fastaFromClustering_forClusterConsensus_MCL( self ):
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270 cDir = os.getcwd()
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271
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272 inFile = "dummyInFaFile_%s" % ( self._uniqId )
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273 inF = open( inFile, "w" )
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274 inF.write( ">MCLCluster8Mb4_seq1\nGTGCGGATGGAACAGT\n" )
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275 inF.write( ">MCLCluster1Mb3_seq2\nATGTACGATGACGATCAG\n" )
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276 inF.close()
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277
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278 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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279 linkF = open( linkFile, "w" )
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280 linkF.write( "seq1\tDHX-incomp_DmelChr4-B-R1-Map4\t1\t18\n" )
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281 linkF.write( "seq2\tRLX-incomp_DmelChr4-B-R12-Map3_reversed\t1\t16\n" )
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282 linkF.write( "seq3\treference2\n" )
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283 linkF.close()
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284
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285 expFile = "dummyExpFile_%s" % ( self._uniqId )
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286 expF = open( expFile, "w" )
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287 expF.write( ">DHX-incomp_MCL8_DmelChr4-B-R1-Map4\nGTGCGGATGGAACAGT\n" )
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288 expF.write( ">RLX-incomp_MCL1_DmelChr4-B-R12-Map3_reversed\nATGTACGATGACGATCAG\n" )
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289 expF.close()
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290
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291 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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292
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293 whichCluster = "B"
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294 cmd = "python ../ChangeSequenceHeaders.py"
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295 cmd += " -i %s" % ( inFile )
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296 cmd += " -f fasta"
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297 cmd += " -s 2"
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298 cmd += " -l %s" % ( linkFile )
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299 cmd += " -w %s" % ( whichCluster )
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300 cmd += " -o %s" % ( obsFile )
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301 exitStatus = os.system( cmd )
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302
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303 self.assertTrue( exitStatus == 0 )
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304 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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305
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306 for f in [ inFile, linkFile, expFile, obsFile ]:
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307 os.remove( f )
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308 os.chdir( cDir )
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309
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310 def test_retrieveInitialSequenceHeaders_newick_script( self ):
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311 cDir = os.getcwd()
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312
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313 inFile = "dummyInFile_%s" % ( self._uniqId )
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314 inF = open( inFile, "w" )
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315 inF.write( "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))" )
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316 inF.close()
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317
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318 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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319 linkF = open( linkFile, "w" )
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320 linkF.write( "seq1\t1360\n" )
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321 linkF.write( "seq2\tDmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies\n" )
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322 linkF.write( "seq3\tDmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies\n" )
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323 linkF.write( "seq4\tDmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies\n" )
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324 linkF.close()
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325
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326 expFile = "dummyExpFile_%s" % ( self._uniqId )
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327 expF = open( expFile, "w" )
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328 expF.write( "(DmelChr4-B-G14-MAP17_classII-TIR-comp|1cl-1gr|41copies:0.012511,(DmelChr4-B-G20-MAP3_classII-TIR-comp|1cl-1gr|53copies:0.005340,DmelChr4-B-P2.0-MAP3_classII-TIR-comp|1cl-1gr|26copies:0.002201))" )
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329 expF.close()
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330
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331 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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332
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333 cmd = "python ../ChangeSequenceHeaders.py"
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334 cmd += " -i %s" % ( inFile )
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335 cmd += " -f newick"
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336 cmd += " -s 2"
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337 cmd += " -l %s" % ( linkFile )
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338 cmd += " -o %s" % ( obsFile )
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339 exitStatus = os.system( cmd )
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340
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341 self.assertTrue( exitStatus == 0 )
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342 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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343
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344 for f in [ inFile, linkFile, expFile, obsFile ]:
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345 os.remove( f )
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346 os.chdir( cDir )
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347
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348
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349 def test_retrieveInitialSequenceHeadersForAlignFile( self ):
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350 cDir = os.getcwd()
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351
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352 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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353 linkF = open( linkFile, "w" )
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354 linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" )
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355 linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" )
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356 linkF.close()
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357
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358 inFile = "dummyAlignFile_%s" % ( self._uniqId )
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359 inFileHandler = open( inFile, "w" )
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360 inFileHandler.write( "seq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" )
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361 inFileHandler.write( "seq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" )
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362 inFileHandler.close()
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363
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364 expFile = "dummyExpAlignFile_%s" % ( self._uniqId )
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365 expFileHandler = open( expFile, "w" )
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366 expFileHandler.write( "name=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" )
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367 expFileHandler.write( "name=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" )
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368 expFileHandler.close()
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369
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370 obsFile = "dummyObsAlignFile_%s" % ( self._uniqId )
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371
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372 cmd = "python ../ChangeSequenceHeaders.py"
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373 cmd += " -i %s" % ( inFile )
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374 cmd += " -f align"
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375 cmd += " -s 2"
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376 cmd += " -l %s" % ( linkFile )
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377 cmd += " -o %s" % ( obsFile )
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378 exitStatus = os.system( cmd )
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379
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380 self.assertTrue( exitStatus == 0 )
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381 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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382
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383 for f in [ inFile, linkFile, expFile, obsFile ]:
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384 os.remove( f )
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385 os.chdir( cDir )
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386
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387
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388 def test_retrieveInitialSequenceHeadersForPathFile( self ):
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389 cDir = os.getcwd()
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390
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391 linkFile = "dummyLinkFile_%s" % ( self._uniqId )
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392 linkF = open( linkFile, "w" )
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393 linkF.write( "seq1\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t1000\n" )
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394 linkF.write( "seq2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t1\t800\n" )
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395 linkF.close()
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396
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397 inFile = "dummyAlignFile_%s" % ( self._uniqId )
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398 inFileHandler = open( inFile, "w" )
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399 inFileHandler.write( "11\tseq1\t1\t100\tseq2\t110\t11\t1e-38\t254\t98.5\n" )
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400 inFileHandler.write( "2\tseq2\t11\t110\tseq1\t100\t1\t1e-38\t254\t98.5\n" )
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401 inFileHandler.close()
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402
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403 expFile = "dummyExpAlignFile_%s" % ( self._uniqId )
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404 expFileHandler = open( expFile, "w" )
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405 expFileHandler.write( "11\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t1\t100\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t110\t11\t1e-38\t254\t98.500000\n" )
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406 expFileHandler.write( "2\tname=Dm_Blaster_Recon_34_Map_20|category=classI|order=LTR|completeness=comp\t11\t110\tname=Dm_Blaster_Piler_30.38_Map_8|category=classI|order=LTR|completeness=comp\t100\t1\t1e-38\t254\t98.500000\n" )
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|
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407 expFileHandler.close()
|
|
|
408
|
|
|
409 obsFile = "dummyObsAlignFile_%s" % ( self._uniqId )
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|
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410
|
|
|
411 cmd = "python ../ChangeSequenceHeaders.py"
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|
|
412 cmd += " -i %s" % ( inFile )
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413 cmd += " -f path"
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414 cmd += " -s 2"
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415 cmd += " -l %s" % ( linkFile )
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416 cmd += " -o %s" % ( obsFile )
|
|
|
417 exitStatus = os.system( cmd )
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|
418
|
|
|
419 self.assertTrue( exitStatus == 0 )
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|
|
420 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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|
|
421
|
|
|
422 for f in [ inFile, linkFile, expFile, obsFile ]:
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|
423 os.remove( f )
|
|
|
424 os.chdir( cDir )
|
|
|
425
|
|
|
426
|
|
|
427 if __name__ == "__main__":
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|
|
428 unittest.main()
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