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Tests for valid RNA Seq bam and warnings when there are no RNA counts
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Wed, 12 Aug 2015 16:28:43 +0100
parents 8e1efafa6277
children 096c6bbf4a04
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5:cef780bcce01 6:2ffa8172dce1
109 """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed.""" 109 """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed."""
110 counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME) 110 counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME)
111 self.assertIsInstance(counts, dict) 111 self.assertIsInstance(counts, dict)
112 self.assertTrue(len(counts) > 0) 112 self.assertTrue(len(counts) > 0)
113 113
114 def test_invalid_rna_file(self):
115 """If an invalid RNA file is provided, generate an error message"""
116 # using transcriptome FASTA file as the invalid RNA file for test
117 parser = riboplot.create_parser()
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, args.ribo_file, args.rna_file)
114 120
115 class RiboPlotTestCase(unittest.TestCase): 121 class RiboPlotTestCase(unittest.TestCase):
116 122
117 def test_get_codon_positions(self): 123 def test_get_codon_positions(self):
118 """Get codon positions in all frames given a sequence.""" 124 """Get codon positions in all frames given a sequence."""
156 162
157 @unittest.skip('todo') 163 @unittest.skip('todo')
158 def test_write_ribo_counts(self): 164 def test_write_ribo_counts(self):
159 """Write RiboSeq read counts as CSV.""" 165 """Write RiboSeq read counts as CSV."""
160 pass 166 pass
161
162 @unittest.skip('todo')
163 def test_plot_read_counts(self):
164 """Generate riboplots"""
165 pass