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comparison tests/test_riboseqr.py @ 0:e01de823e919 draft default tip

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author biotechcoder
date Fri, 01 May 2015 05:41:51 -0400
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1 """riboSeqR Galaxy unit tests"""
2 import sys
3 import unittest
4 import rpy2.robjects as robjects
5 from riboseqr import prepare, triplet, metagene, ribosome_profile, utils
6
7
8 R = robjects.r
9 DATA_DIR = 'test-data'
10 RIBO_FILES = ', '.join(
11 '{0}/{1}'.format(DATA_DIR, item) for item in
12 ['chlamy236_plus_deNovo_plusOnly_Index17',
13 'chlamy236_plus_deNovo_plusOnly_Index3',
14 'chlamy236_plus_deNovo_plusOnly_Index5',
15 'chlamy236_plus_deNovo_plusOnly_Index7'])
16
17 RNA_FILES = ', '.join(
18 '{0}/{1}'.format(DATA_DIR, item) for item in
19 ['chlamy236_plus_deNovo_plusOnly_Index10',
20 'chlamy236_plus_deNovo_plusOnly_Index12',
21 'chlamy236_plus_deNovo_plusOnly_Index14',
22 'chlamy236_plus_deNovo_plusOnly_Index16'])
23
24 FASTA_FILE = '{0}/{1}'.format(DATA_DIR, 'rsem_chlamy236_deNovo.transcripts.fa')
25
26
27 class PrepareTestCase(unittest.TestCase):
28
29 def test_process_riboseqr_input(self):
30 """Given riboSeqR format input files (bowtie output), save ribodata to \
31 an R data file.
32
33 """
34 do_prepare()
35 R('load("{}/Robjects.rda")'.format(DATA_DIR))
36 ribodat, ribodat_ref = R['riboDat'], R['riboDat_REF']
37
38 self.assertEqual(
39 '{}'.format(ribodat), '{}'.format(ribodat_ref),
40 'Generated RiboDat object must be equal to the reference')
41
42 def test_process_args(self):
43 """Test processing arguments. """
44 # "ATG" -> c("ATG")
45 rs = utils.process_args('ATG', ret_mode='charvector')
46 self.assertEqual(rs, 'c("ATG")','Return string as a character vector.')
47
48 # stop codons "TAG,TAA,TGA" -> c("TAG", "TAA", "TGA"). Also
49 # replicate names, seqnames.
50 rs = utils.process_args('TAG,TAA,TGA', ret_mode='charvector')
51 self.assertEqual(
52 rs, "c('TAG', 'TAA', 'TGA')",
53 'Return comma separated strings as a character vector.')
54
55 # "" -> None
56 rs = utils.process_args('')
57 self.assertIsNone(rs, 'Return empty string as None.')
58
59 # "27,28" -> c(27, 28)
60 rs = utils.process_args("27,28", ret_type='int', ret_mode='charvector')
61 self.assertEqual(
62 rs, "c(27, 28)", 'Return number strings as a character vector.')
63
64 # "27,28" -> [27, 28]
65 rs = utils.process_args("27,28", ret_type='int', ret_mode='list')
66 self.assertEqual(rs, [27, 28], 'Return number strings as a list.')
67
68 # "0,2" -> list(0,2)
69 rs = utils.process_args("0,2", ret_type='int', ret_mode='listvector')
70 self.assertEqual(
71 rs, "list(0, 2)", 'Return number strings as a list vector.')
72
73 # "50" -> 50
74 rs = utils.process_args("50", ret_type='int')
75 self.assertEqual(rs, 50, 'Return number string as a number.')
76
77 # "-200" -> -200
78 rs = utils.process_args("-200", ret_type='int')
79 self.assertEqual(rs, -200, 'Return number string as a number.')
80
81 # "TRUE" -> TRUE
82 rs = utils.process_args("TRUE", ret_type='bool')
83 self.assertEqual(rs, 'TRUE', 'Return bool string as bool.')
84
85 # 'chlamy17,chlamy3' -> 'chlamy17,chlamy3' for ribo and rna names
86 rs = utils.process_args('chlamy17,chlamy3')
87 self.assertEqual(rs, 'chlamy17,chlamy3', 'Return csv string as string.')
88
89 # 'chlamy17.idx, chlamy3.idx' -> ['chlamy17.idx', 'chlamy3.idx']
90 rs = utils.process_args('chlamy17.idx, chlamy3.idx', ret_mode='list')
91 self.assertEqual(rs, ['chlamy17.idx', 'chlamy3.idx'],
92 'Return files as a list.')
93
94
95 class TripletTestCase(unittest.TestCase):
96
97 def test_find_periodicity(self):
98 """Test triplet periodicity. """
99 do_prepare()
100 do_periodicity()
101 fcs, fs, fasta_cds = R['fCs'], R['fS'], R['fastaCDS']
102
103 R('load("{}/Robjects.rda")'.format(DATA_DIR))
104 fcs_ref, fs_ref, fasta_cds_ref = (
105 R['fCs_REF'], R['fS_REF'], R['fastaCDS_REF'])
106
107 self.assertEqual(
108 (str(fcs), str(fs), str(fasta_cds)),
109 (str(fcs_ref), str(fs_ref), str(fasta_cds_ref)),
110 msg='Generated fCs, fS and fastaCDS objects must be equal '
111 'to reference')
112
113
114 class MetageneTestCase(unittest.TestCase):
115
116 def test_do_analysis(self):
117 """Test metagene analysis. """
118 R('load("{}/Robjects.rda")'.format(DATA_DIR))
119 do_prepare()
120 do_periodicity()
121 do_metagene()
122
123 self.assertEqual(str(R['ffCs']),
124 str(R['ffCs_REF']), 'ffCs must be equal to reference')
125
126
127 def do_prepare():
128 """Run the prepare step to generate riboDat from input files."""
129 prepare.generate_ribodata(
130 ribo_files=RIBO_FILES, rna_files=RNA_FILES, replicate_names='WT,WT,M,M',
131 rdata_save='/tmp/Prepare.rda', sam_format=False, output_path="/tmp",
132 html_file='/tmp/Prepare-report.html')
133
134
135 def do_periodicity():
136 """Run the periodicity step"""
137 triplet.find_periodicity(
138 rdata_load='/tmp/Prepare.rda', start_codons='ATG',
139 stop_codons='TAG,TAA,TGA', fasta_file=FASTA_FILE,
140 include_lengths='25:30', analyze_plot_lengths='26:30',
141 rdata_save='/tmp/Periodicity.rda', output_path="/tmp",
142 html_file='/tmp/Periodicity-report.html')
143
144
145 def do_metagene():
146 """Run the metagene step"""
147 metagene.do_analysis(
148 rdata_load='/tmp/Periodicity.rda', selected_lengths='27,28',
149 selected_frames='1,0', hit_mean='50', unique_hit_mean='10',
150 ratio_check='TRUE', min5p='-20', max5p='200', min3p='-200', max3p='20',
151 cap='200', plot_title='Metagene analysis', plot_lengths='27',
152 rdata_save='/tmp/Metagene.rda', output_path="/tmp",
153 html_file='/tmp/Metagene-report.html')