comparison tests/test_riboplot.py @ 14:628f82e72d72

Version as released on PyPI 0.1.0

13:8a87a2c44d09

# use testing configuration
CONFIG = riboplot.CONFIG = riboplot.config.TestingConfig()
logging.disable(logging.CRITICAL)

RIBO_FILE = os.path.join(CONFIG.DATA_DIR, '5hRPFsorted.bam')
RNA_FILE = os.path.join(CONFIG.DATA_DIR, '5hmRNAsorted.bam')
TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|'
TRANSCRIPTOME_FASTA = os.path.join(CONFIG.DATA_DIR, 'zebrafish.fna')
TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.DATA_DIR, 'zebrafish_minus1.fna')


class CheckArgumentsTestCase(unittest.TestCase):
    """Check if all arguments sent on the command line are valid."""
    parser = riboplot.create_parser()

                          args.ribo_file, args.transcriptome_fasta, 'hello')

    def test_missing_transcript_in_bam(self):
        """If a transcript is missing in BAM, an error is raised."""
        # testing with an unrelated BAM file
        args = self.parser.parse_args(['-b', '/home/vimal/tmp/empty_tp/RiboSeq.bam', '-f', TRANSCRIPTOME_FASTA,
                                       '-t', TRANSCRIPT_NAME])
        self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, args.ribo_file,
                          args.transcriptome_fasta, args.transcript_name)

14:628f82e72d72

# use testing configuration
CONFIG = riboplot.CONFIG = riboplot.config.TestingConfig()
logging.disable(logging.CRITICAL)

RIBO_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hRPFsorted.bam')
RNA_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hmRNAsorted.bam')
TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|'
TRANSCRIPTOME_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish.fna')
UNRELATED_BAM = os.path.join(CONFIG.TEST_DATA_DIR, 'unrelated.bam')


class CheckArgumentsTestCase(unittest.TestCase):
    """Check if all arguments sent on the command line are valid."""
    parser = riboplot.create_parser()

                          args.ribo_file, args.transcriptome_fasta, 'hello')

    def test_missing_transcript_in_bam(self):
        """If a transcript is missing in BAM, an error is raised."""
        # testing with an unrelated BAM file
        args = self.parser.parse_args(['-b', UNRELATED_BAM, '-f', TRANSCRIPTOME_FASTA,
                                       '-t', TRANSCRIPT_NAME])
        self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, args.ribo_file,
                          args.transcriptome_fasta, args.transcript_name)