Ejemplo n.º 1
0
    def test_allup(self):
        """ runs entire program on small test dataset """

        args = [
            "--clusters",
            pkg_resources.resource_filename(__name__,
                                            "../test/fox_2_test.BED"),
            "-s",
            "mm9",
            "--bam",
            pkg_resources.resource_filename(__name__,
                                            "../test/FOX2Brain.all.bam"),
            "--AS_Structure",
            "/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9data4",
            '--genome_location',
            '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9/mm9.fa',
            "--regions_location",
            '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/regions',
            '--phastcons_location',
            '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/phastcons/mm9_phastcons.bw',
            '--motif',
            'AAAAAA',
            '--nrand',
            '1',
        ]
        (options, args) = self.parser.parse_args(args)
        CLIP_analysis.main(options)
Ejemplo n.º 2
0
 def test_allup(self):
     
     """ runs entire program on small test dataset """
     
     args = ["--clusters", pkg_resources.resource_filename(__name__, "../test/fox_2_test.BED"),
             "-s", "mm9",
             "--bam", pkg_resources.resource_filename(__name__, "../test/FOX2Brain.all.bam"),
             "--AS_Structure", "/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9data4",
             '--genome_location', '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9/mm9.fa', 
             "--regions_location", '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/regions',
             '--phastcons_location', '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/phastcons/mm9_phastcons.bw',
             '--motif', 'AAAAAA',
             '--nrand', '1',
             ]    
     (options, args) = self.parser.parse_args(args)
     CLIP_analysis.main(options)
Ejemplo n.º 3
0
    def test_allup(self):
        
        """ runs entire program on small test dataset """

        args = ["--clusters", clipper.test_file("clip_analysis_test_peak_results.bed"),
                "-s", "mm9",
                "--bam", clipper.test_file("allup_test.bam"),
                "--AS_Structure", "/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9data4",
                '--genome_location', '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/mm9/mm9.fa', 
                "--regions_location", '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/regions',
                '--phastcons_location', '/home/gabrielp/bioinformatics/Yeo_Lab/clip_analysis_metadata/phastcons/mm9_phastcons.bw',
                '--motif', 'AAAAAA',
                '--nrand', '1',
                '--rePhast',
                '--runPhast'
                ]    
        (options, args) = self.parser.parse_args(args)
        CLIP_analysis.main(options)