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)