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)
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)
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)