comparison tests/test_riboplot.py @ 12:61c47a1d6a7a

Add a test to check if a valid FASTA file is used (ribocount)

11:7571f5c89090

        # 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, ribo_file=args.ribo_file, rna_file=args.rna_file)

class RiboPlotTestCase(unittest.TestCase):

    def test_get_codon_positions(self):
        """Get codon positions in all frames given a sequence."""
        # the positions on this sequence were calculated manually.

            self.assertTrue(os.path.exists(os.path.join(output_dir, fname)))
        shutil.rmtree(output_dir)

    def test_transcript_with_no_counts(self):
        """If the transcript has no ribocounts, no plot should be produced."""
        transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads
        output_dir = tempfile.mkdtemp()
        parser = riboplot.create_parser()
        args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir])
        self.assertRaises(ribocore.RiboPlotError, riboplot.main, args)
        for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
            self.assertFalse(os.path.exists(os.path.join(output_dir, fname)))
        shutil.rmtree(output_dir)

    @unittest.skip('todo')
    def test_get_ribo_counts(self):
        """Get RiboSeq read counts"""
        pass

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

12:61c47a1d6a7a

        # 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, ribo_file=args.ribo_file, rna_file=args.rna_file)


class RiboPlotTestCase(unittest.TestCase):

    def test_get_codon_positions(self):
        """Get codon positions in all frames given a sequence."""
        # the positions on this sequence were calculated manually.

            self.assertTrue(os.path.exists(os.path.join(output_dir, fname)))
        shutil.rmtree(output_dir)

    def test_transcript_with_no_counts(self):
        """If the transcript has no ribocounts, no plot should be produced."""
        transcript = 'gi|62955616|ref|NM_001017822.1|'  # has no reads
        output_dir = tempfile.mkdtemp()
        parser = riboplot.create_parser()
        args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir])
        self.assertRaises(ribocore.RiboPlotError, riboplot.main, args)
        for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
            self.assertFalse(os.path.exists(os.path.join(output_dir, fname)))
        shutil.rmtree(output_dir)