def test_target_gene(self):
peaks_path = 'Ese14_H3K27ac_LICR_Rep2_peaks_200.xls'
genome_path = '/home/jiawei/.MotifScan/genome/mm9'
gene_path = '/home/jiawei/.MotifScan/gene/mm9/refSeq.txt'
print "loading genes"
gene_table = peak.load_ref_gene(gene_path)
print "loading peaks"
peak_table = peak.load_peak(peaks_path,genome_path,1000,'macs')
peak.extract_target_gene(peak_table, gene_table)
motifscan_general.motif_sc
def test_load_peak(self):
#peaks_path = 'H3K4me3_H1hesc_VS_K562_all_peak_MAvalues_3peaks.xls'
peaks_path = 'Ese14_H3K27ac_LICR_Rep2_peaks.xls'
genome_path = '/home/jiawei/.MotifScan/genome/mm9'
gene_path = '/home/jiawei/.MotifScan/gene/mm9/refSeq.txt'
print "loading genes"
gene_table = peak.load_ref_gene(gene_path)
print "loading peaks"
peak_table = peak.load_peak(peaks_path,genome_path,1000,'macs')
print "generate randoms"
peak.generate_random_with_ref2(gene_table,peak_table,genome_path,1)
def test_motif_scan(self):
peak_path = 'Ese14_H3K27ac_LICR_Rep2_peaks.xls'
p = peak.load_peak(peak_path,'/home/jiawei/.MotifScan/genome/hg19',1000,'macs')
m = motif.load_motif('/mnt/MAmotif/motifscan_pkg/MotifScan/motif_list/jaspar_2014_vertebrates_motif_list.txt','/mnt/MAmotif/motifscan_pkg/MotifScan/motif/mm9/mm9_jaspar_2014_all_1e-4.txt')
core.motif_scan(p,m,np.array([0.29,0.21,0.21,0.29]),'./tmp')
