comparison tests/test_riboplot.py @ 7:096c6bbf4a04

Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments

6:2ffa8172dce1

        """If bedtools is not in PATH, raise an error."""
        args = self.parser.parse_args(
            ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE])
        save_path = os.environ['PATH']
        os.environ['PATH'] = ''
        self.assertRaises(OSError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file)
        os.environ['PATH'] = save_path

    def test_is_bam_valid(self):
        """Test if BAM file is valid."""
        valid = ribocore.is_bam_valid(RIBO_FILE)

    def test_invalid_read_length(self):
        """An error is raised if an invalid read length is used."""
        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-l', '-1'])  # invalid read length -1
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          args.ribo_file, None, args.read_length)

        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-l', '100'])  # invalid read length 100
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          args.ribo_file, None, args.read_length)

    def test_valid_read_offset(self):
        """Read offset should be positive."""
        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-s', '-1'])  # invalid read offset -1
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          args.ribo_file, None, None, args.read_offset)

    def test_is_fasta_valid(self):
        """A valid FASTA file can be opened with pysam.FastaFile."""
        self.assertTrue(ribocore.is_fasta_valid(TRANSCRIPTOME_FASTA))

    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."""

7:096c6bbf4a04

        """If bedtools is not in PATH, raise an error."""
        args = self.parser.parse_args(
            ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE])
        save_path = os.environ['PATH']
        os.environ['PATH'] = ''
        self.assertRaises(OSError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file)
        os.environ['PATH'] = save_path

    def test_is_bam_valid(self):
        """Test if BAM file is valid."""
        valid = ribocore.is_bam_valid(RIBO_FILE)

    def test_invalid_read_length(self):
        """An error is raised if an invalid read length is used."""
        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-l', '-1'])  # invalid read length -1
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          ribo_file=args.ribo_file, read_length=args.read_length)

        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-l', '100'])  # invalid read length 100
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          ribo_file=args.ribo_file, read_length=args.read_length)

    def test_valid_read_offset(self):
        """Read offset should be positive."""
        args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                       '-s', '-1'])  # invalid read offset -1
        self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
                          ribo_file=args.ribo_file, read_offset=args.read_offset)

    def test_is_fasta_valid(self):
        """A valid FASTA file can be opened with pysam.FastaFile."""
        self.assertTrue(ribocore.is_fasta_valid(TRANSCRIPTOME_FASTA))

    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, 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."""