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comparison tests/test_riboplot.py @ 12:61c47a1d6a7a

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Add a test to check if a valid FASTA file is used (ribocount)
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Wed, 19 Aug 2015 11:11:37 +0100
parents 096c6bbf4a04
children 628f82e72d72
comparison
equal deleted inserted replaced
11:7571f5c89090 12:61c47a1d6a7a
116 # using transcriptome FASTA file as the invalid RNA file for test 116 # using transcriptome FASTA file as the invalid RNA file for test
117 parser = riboplot.create_parser() 117 parser = riboplot.create_parser()
118 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA]) 118 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA])
119 self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) 119 self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file)
120 120
121
121 class RiboPlotTestCase(unittest.TestCase): 122 class RiboPlotTestCase(unittest.TestCase):
122 123
123 def test_get_codon_positions(self): 124 def test_get_codon_positions(self):
124 """Get codon positions in all frames given a sequence.""" 125 """Get codon positions in all frames given a sequence."""
125 # the positions on this sequence were calculated manually. 126 # the positions on this sequence were calculated manually.
144 self.assertTrue(os.path.exists(os.path.join(output_dir, fname))) 145 self.assertTrue(os.path.exists(os.path.join(output_dir, fname)))
145 shutil.rmtree(output_dir) 146 shutil.rmtree(output_dir)
146 147
147 def test_transcript_with_no_counts(self): 148 def test_transcript_with_no_counts(self):
148 """If the transcript has no ribocounts, no plot should be produced.""" 149 """If the transcript has no ribocounts, no plot should be produced."""
149 transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads 150 transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads
150 output_dir = tempfile.mkdtemp() 151 output_dir = tempfile.mkdtemp()
151 parser = riboplot.create_parser() 152 parser = riboplot.create_parser()
152 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir]) 153 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir])
153 self.assertRaises(ribocore.RiboPlotError, riboplot.main, args) 154 self.assertRaises(ribocore.RiboPlotError, riboplot.main, args)
154 for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'): 155 for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
155 self.assertFalse(os.path.exists(os.path.join(output_dir, fname))) 156 self.assertFalse(os.path.exists(os.path.join(output_dir, fname)))
156 shutil.rmtree(output_dir) 157 shutil.rmtree(output_dir)
157
158 @unittest.skip('todo')
159 def test_get_ribo_counts(self):
160 """Get RiboSeq read counts"""
161 pass
162
163 @unittest.skip('todo')
164 def test_write_ribo_counts(self):
165 """Write RiboSeq read counts as CSV."""
166 pass