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1 """riboSeqR Galaxy unit tests"""
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2 import sys
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3 import unittest
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4 import rpy2.robjects as robjects
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5 from riboseqr import prepare, triplet, metagene, ribosome_profile, utils
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6
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7
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8 R = robjects.r
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9 DATA_DIR = 'test-data'
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10 RIBO_FILES = ', '.join(
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11 '{0}/{1}'.format(DATA_DIR, item) for item in
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12 ['chlamy236_plus_deNovo_plusOnly_Index17',
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13 'chlamy236_plus_deNovo_plusOnly_Index3',
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14 'chlamy236_plus_deNovo_plusOnly_Index5',
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15 'chlamy236_plus_deNovo_plusOnly_Index7'])
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16
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17 RNA_FILES = ', '.join(
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18 '{0}/{1}'.format(DATA_DIR, item) for item in
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19 ['chlamy236_plus_deNovo_plusOnly_Index10',
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20 'chlamy236_plus_deNovo_plusOnly_Index12',
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21 'chlamy236_plus_deNovo_plusOnly_Index14',
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22 'chlamy236_plus_deNovo_plusOnly_Index16'])
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23
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24 FASTA_FILE = '{0}/{1}'.format(DATA_DIR, 'rsem_chlamy236_deNovo.transcripts.fa')
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25
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26
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27 class PrepareTestCase(unittest.TestCase):
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28
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29 def test_process_riboseqr_input(self):
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30 """Given riboSeqR format input files (bowtie output), save ribodata to \
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31 an R data file.
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32
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33 """
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34 do_prepare()
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35 R('load("{}/Robjects.rda")'.format(DATA_DIR))
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36 ribodat, ribodat_ref = R['riboDat'], R['riboDat_REF']
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37
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38 self.assertEqual(
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39 '{}'.format(ribodat), '{}'.format(ribodat_ref),
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40 'Generated RiboDat object must be equal to the reference')
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41
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42 def test_process_args(self):
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43 """Test processing arguments. """
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44 # "ATG" -> c("ATG")
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45 rs = utils.process_args('ATG', ret_mode='charvector')
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46 self.assertEqual(rs, 'c("ATG")','Return string as a character vector.')
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47
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48 # stop codons "TAG,TAA,TGA" -> c("TAG", "TAA", "TGA"). Also
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49 # replicate names, seqnames.
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50 rs = utils.process_args('TAG,TAA,TGA', ret_mode='charvector')
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51 self.assertEqual(
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52 rs, "c('TAG', 'TAA', 'TGA')",
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53 'Return comma separated strings as a character vector.')
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54
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55 # "" -> None
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56 rs = utils.process_args('')
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57 self.assertIsNone(rs, 'Return empty string as None.')
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58
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59 # "27,28" -> c(27, 28)
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60 rs = utils.process_args("27,28", ret_type='int', ret_mode='charvector')
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61 self.assertEqual(
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62 rs, "c(27, 28)", 'Return number strings as a character vector.')
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63
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64 # "27,28" -> [27, 28]
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65 rs = utils.process_args("27,28", ret_type='int', ret_mode='list')
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66 self.assertEqual(rs, [27, 28], 'Return number strings as a list.')
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67
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68 # "0,2" -> list(0,2)
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69 rs = utils.process_args("0,2", ret_type='int', ret_mode='listvector')
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70 self.assertEqual(
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71 rs, "list(0, 2)", 'Return number strings as a list vector.')
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72
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73 # "50" -> 50
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74 rs = utils.process_args("50", ret_type='int')
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75 self.assertEqual(rs, 50, 'Return number string as a number.')
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76
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77 # "-200" -> -200
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78 rs = utils.process_args("-200", ret_type='int')
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79 self.assertEqual(rs, -200, 'Return number string as a number.')
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80
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81 # "TRUE" -> TRUE
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82 rs = utils.process_args("TRUE", ret_type='bool')
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83 self.assertEqual(rs, 'TRUE', 'Return bool string as bool.')
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84
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85 # 'chlamy17,chlamy3' -> 'chlamy17,chlamy3' for ribo and rna names
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86 rs = utils.process_args('chlamy17,chlamy3')
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87 self.assertEqual(rs, 'chlamy17,chlamy3', 'Return csv string as string.')
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88
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89 # 'chlamy17.idx, chlamy3.idx' -> ['chlamy17.idx', 'chlamy3.idx']
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90 rs = utils.process_args('chlamy17.idx, chlamy3.idx', ret_mode='list')
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91 self.assertEqual(rs, ['chlamy17.idx', 'chlamy3.idx'],
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92 'Return files as a list.')
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93
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94
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95 class TripletTestCase(unittest.TestCase):
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96
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97 def test_find_periodicity(self):
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98 """Test triplet periodicity. """
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99 do_prepare()
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100 do_periodicity()
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101 fcs, fs, fasta_cds = R['fCs'], R['fS'], R['fastaCDS']
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102
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103 R('load("{}/Robjects.rda")'.format(DATA_DIR))
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104 fcs_ref, fs_ref, fasta_cds_ref = (
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105 R['fCs_REF'], R['fS_REF'], R['fastaCDS_REF'])
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106
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107 self.assertEqual(
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108 (str(fcs), str(fs), str(fasta_cds)),
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109 (str(fcs_ref), str(fs_ref), str(fasta_cds_ref)),
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110 msg='Generated fCs, fS and fastaCDS objects must be equal '
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111 'to reference')
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112
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113
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114 class MetageneTestCase(unittest.TestCase):
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115
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116 def test_do_analysis(self):
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117 """Test metagene analysis. """
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118 R('load("{}/Robjects.rda")'.format(DATA_DIR))
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119 do_prepare()
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120 do_periodicity()
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121 do_metagene()
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122
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123 self.assertEqual(str(R['ffCs']),
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124 str(R['ffCs_REF']), 'ffCs must be equal to reference')
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125
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126
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127 def do_prepare():
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128 """Run the prepare step to generate riboDat from input files."""
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129 prepare.generate_ribodata(
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130 ribo_files=RIBO_FILES, rna_files=RNA_FILES, replicate_names='WT,WT,M,M',
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131 rdata_save='/tmp/Prepare.rda', sam_format=False, output_path="/tmp",
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132 html_file='/tmp/Prepare-report.html')
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133
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134
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135 def do_periodicity():
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136 """Run the periodicity step"""
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137 triplet.find_periodicity(
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138 rdata_load='/tmp/Prepare.rda', start_codons='ATG',
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139 stop_codons='TAG,TAA,TGA', fasta_file=FASTA_FILE,
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140 include_lengths='25:30', analyze_plot_lengths='26:30',
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141 rdata_save='/tmp/Periodicity.rda', output_path="/tmp",
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142 html_file='/tmp/Periodicity-report.html')
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143
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144
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145 def do_metagene():
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146 """Run the metagene step"""
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147 metagene.do_analysis(
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148 rdata_load='/tmp/Periodicity.rda', selected_lengths='27,28',
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149 selected_frames='1,0', hit_mean='50', unique_hit_mean='10',
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150 ratio_check='TRUE', min5p='-20', max5p='200', min3p='-200', max3p='20',
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151 cap='200', plot_title='Metagene analysis', plot_lengths='27',
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152 rdata_save='/tmp/Metagene.rda', output_path="/tmp",
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153 html_file='/tmp/Metagene-report.html')
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