Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_PslParser.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 from commons.core.parsing.PslParser import PslParser
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2 import unittest, os
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3
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4
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5 class Test_PslParser(unittest.TestCase):
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6
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7 def test_forward(self):
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8 fileName = "tmpFile.psl"
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9 handle = open(fileName, "w")
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10 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\T\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n158\t0\t0\t0\t0\t0\t1\t158\t+\ttest\t158\t0\t158\tchr1\t1501\t237\t553\t2\t79,79,\t0,79,\t237,474,\n")
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11 handle.close()
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12
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13 parser = PslParser(fileName, 0)
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14 self.assertEquals(parser.getNbMappings(), 1)
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15 for mapping in parser.getIterator():
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16 transcript = mapping.getTranscript()
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17 self.assertEquals(transcript.getName(), "test")
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18 self.assertEquals(transcript.getChromosome(), "chr1")
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19 self.assertEquals(transcript.getDirection(), 1)
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20 self.assertEquals(transcript.getStart(), 238)
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21 self.assertEquals(transcript.getEnd(), 553)
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22 self.assertEquals(transcript.getNbExons(), 2)
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23 for i, exon in enumerate(transcript.getExons()):
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24 if i == 0:
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25 self.assertEquals(exon.getStart(), 238)
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26 self.assertEquals(exon.getEnd(), 316)
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27 elif i == 1:
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28 self.assertEquals(exon.getStart(), 475)
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29 self.assertEquals(exon.getEnd(), 553)
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30 os.remove(fileName)
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31
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32
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33 def test_backward(self):
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34 fileName = "tmpFile.psl"
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35 handle = open(fileName, "w")
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36 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\tT\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n158\t0\t0\t0\t0\t0\t1\t158\t-\ttest\t158\t0\t158\tchr1\t1501\t237\t553\t2\t79,79,\t0,79,\t237,474,\n")
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37
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38 handle.close()
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39
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40 parser = PslParser(fileName, 0)
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41 self.assertEquals(parser.getNbMappings(), 1)
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42 for mapping in parser.getIterator():
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43 transcript = mapping.getTranscript()
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44 self.assertEquals(transcript.getName(), "test")
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45 self.assertEquals(transcript.getChromosome(), "chr1")
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46 self.assertEquals(transcript.getDirection(), -1)
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47 self.assertEquals(transcript.getStart(), 238)
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48 self.assertEquals(transcript.getEnd(), 553)
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49 self.assertEquals(transcript.getNbExons(), 2)
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50 for i, exon in enumerate(transcript.getExons()):
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51 if i == 1:
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52 self.assertEquals(exon.getStart(), 238)
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53 self.assertEquals(exon.getEnd(), 316)
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54 elif i == 0:
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55 self.assertEquals(exon.getStart(), 475)
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56 self.assertEquals(exon.getEnd(), 553)
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57 os.remove(fileName)
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58
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59
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60 def test_query_forward_target_forward(self):
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61 fileName = "tmpFile.psl"
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62 handle = open(fileName, "w")
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63 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\tT\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n241\t0\t0\t0\t0\t0\t1\t60\t++\tseq1\t255\t9\t250\tref\t2262\t59\t360\t2\t121,120,\t9,130,\t59,240,\n")
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64 handle.close()
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65
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66 parser = PslParser(fileName, 0)
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67 self.assertEquals(parser.getNbMappings(), 1)
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68 for mapping in parser.getIterator():
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69 transcript = mapping.getTranscript()
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70 self.assertEquals(transcript.getName(), "seq1")
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71 self.assertEquals(transcript.getChromosome(), "ref")
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72 self.assertEquals(transcript.getDirection(), 1)
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73 self.assertEquals(transcript.getStart(), 60)
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74 self.assertEquals(transcript.getEnd(), 360)
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75 self.assertEquals(transcript.getNbExons(), 2)
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76 for i, exon in enumerate(transcript.getExons()):
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77 if i == 0:
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78 self.assertEquals(exon.getStart(), 60)
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79 self.assertEquals(exon.getEnd(), 180)
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80 elif i == 1:
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81 self.assertEquals(exon.getStart(), 241)
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82 self.assertEquals(exon.getEnd(), 360)
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83 os.remove(fileName)
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84
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85 def test_query_backward_target_forward(self):
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86 fileName = "tmpFile.psl"
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87 handle = open(fileName, "w")
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88 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\tT\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n241\t0\t0\t0\t0\t0\t1\t60\t-+\tseq2\t255\t5\t246\tref\t2262\t59\t360\t2\t121,120,\t9,130,\t59,240,\n")
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89 handle.close()
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90
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91 parser = PslParser(fileName, 0)
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92 self.assertEquals(parser.getNbMappings(), 1)
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93 for mapping in parser.getIterator():
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94 transcript = mapping.getTranscript()
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95 self.assertEquals(transcript.getName(), "seq2")
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96 self.assertEquals(transcript.getChromosome(), "ref")
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97 self.assertEquals(transcript.getDirection(), -1)
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98 self.assertEquals(transcript.getStart(), 60)
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99 self.assertEquals(transcript.getEnd(), 360)
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100 self.assertEquals(transcript.getNbExons(), 2)
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101 for i, exon in enumerate(transcript.getExons()):
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102 if i == 1:
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103 self.assertEquals(exon.getStart(), 60)
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104 self.assertEquals(exon.getEnd(), 180)
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105 elif i == 0:
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106 self.assertEquals(exon.getStart(), 241)
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107 self.assertEquals(exon.getEnd(), 360)
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108 os.remove(fileName)
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109
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110 def test_query_backward_target_backward(self):
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111 fileName = "tmpFile.psl"
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112 handle = open(fileName, "w")
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113 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\tT\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n241\t1\t0\t0\t0\t0\t1\t60\t--\tseq1\t255\t8\t250\tref\t2262\t58\t360\t2\t120,122,\t5,125,\t1902,2082,\n")
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114 handle.close()
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115
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116 parser = PslParser(fileName, 0)
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117 self.assertEquals(parser.getNbMappings(), 1)
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118 for mapping in parser.getIterator():
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119 transcript = mapping.getTranscript()
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120 self.assertEquals(transcript.getName(), "seq1")
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121 self.assertEquals(transcript.getChromosome(), "ref")
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122 self.assertEquals(transcript.getDirection(), 1)
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123 self.assertEquals(transcript.getStart(), 59)
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124 self.assertEquals(transcript.getEnd(), 360)
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125 self.assertEquals(transcript.getNbExons(), 2)
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126 for i, exon in enumerate(transcript.getExons()):
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127 if i == 0:
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128 self.assertEquals(exon.getStart(), 59)
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129 self.assertEquals(exon.getEnd(), 180)
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130 elif i == 1:
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131 self.assertEquals(exon.getStart(), 241)
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132 self.assertEquals(exon.getEnd(), 360)
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133 os.remove(fileName)
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134
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135
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136 def test_query_forward_target_backward(self):
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137 fileName = "tmpFile.psl"
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138 handle = open(fileName, "w")
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139 handle.write("psLayout version 3\n\nmatch\tmis-\trep.\tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ\tQ\tQ\tQ\tT\tT\tT\tT\tblock\tblockSizes\tqStarts\ttStarts\nmatch\tmatch\tcount\tbases\tcount\tbases\tname\tsize\tstart\tend\tname\tsize\tstart\tend\tcount\n---------------------------------------------------------------------------------------------------------------------------------------------------------------\n241\t1\t0\t0\t0\t0\t1\t60\t+-\tseq2\t255\t5\t247\tref\t2262\t58\t360\t2\t120,122,\t5,125,\t1902,2082,\n")
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140 handle.close()
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141
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142 parser = PslParser(fileName, 0)
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143 self.assertEquals(parser.getNbMappings(), 1)
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144 for mapping in parser.getIterator():
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145 transcript = mapping.getTranscript()
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146 self.assertEquals(transcript.getName(), "seq2")
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147 self.assertEquals(transcript.getChromosome(), "ref")
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148 self.assertEquals(transcript.getDirection(), -1)
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149 self.assertEquals(transcript.getStart(), 59)
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150 self.assertEquals(transcript.getEnd(), 360)
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151 self.assertEquals(transcript.getNbExons(), 2)
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152 for i, exon in enumerate(transcript.getExons()):
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153 if i == 1:
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154 self.assertEquals(exon.getStart(), 59)
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155 self.assertEquals(exon.getEnd(), 180)
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156 elif i == 0:
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157 self.assertEquals(exon.getStart(), 241)
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158 self.assertEquals(exon.getEnd(), 360)
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159 os.remove(fileName)
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160
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161
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162 if __name__ == "__main__":
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163 unittest.main()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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164
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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165