comparison tests/test_riboplot.py @ 6:2ffa8172dce1

Tests for valid RNA Seq bam and warnings when there are no RNA counts

5:cef780bcce01

        """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed."""
        counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME)
        self.assertIsInstance(counts, dict)
        self.assertTrue(len(counts) > 0)


class RiboPlotTestCase(unittest.TestCase):

    def test_get_codon_positions(self):
        """Get codon positions in all frames given a sequence."""

    @unittest.skip('todo')
    def test_write_ribo_counts(self):
        """Write RiboSeq read counts as CSV."""
        pass

    @unittest.skip('todo')
    def test_plot_read_counts(self):
        """Generate riboplots"""
        pass

6:2ffa8172dce1

        """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed."""
        counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME)
        self.assertIsInstance(counts, dict)
        self.assertTrue(len(counts) > 0)

    def test_invalid_rna_file(self):
        """If an invalid RNA file is provided, generate an error message"""
        # using transcriptome FASTA file as the invalid RNA file for test
        parser = riboplot.create_parser()
        args = parser.parse_args(['-b', RIBO_FILE,  '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA])
        self.assertRaises(ValueError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file)

class RiboPlotTestCase(unittest.TestCase):

    def test_get_codon_positions(self):
        """Get codon positions in all frames given a sequence."""

    @unittest.skip('todo')
    def test_write_ribo_counts(self):
        """Write RiboSeq read counts as CSV."""
        pass