def test_fc_plot(self): p1 = pd.read_pickle('MAmotif_test_input/h1hesc_peak_result.pkl') r1 = pd.read_pickle('MAmotif_test_input/h1hesc_rnd_result.pkl') e1 = pd.read_pickle('MAmotif_test_input/h1hesc_enrich_result.pkl') p2 = pd.read_pickle('MAmotif_test_input/k562_peak_result.pkl') r2 = pd.read_pickle('MAmotif_test_input/k562_rnd_result.pkl') e2 = pd.read_pickle('MAmotif_test_input/k562_enrich_result.pkl') p3 = pd.read_pickle('MAmotif_test_input/common_peak_result.pkl') r3 = pd.read_pickle('MAmotif_test_input/common_rnd_result.pkl') e3 = pd.read_pickle('MAmotif_test_input/common_enrich_result.pkl') [p,r,e] = motifscan_general.merge_two_results(p1,p2,r1,r2,e1) [p,r,e] = motifscan_general.merge_two_results(p,p3,r,r3,e3) core.fc_plot(p,r,'./test_fc_plot')
def test_peak_set_enrichemnt_analysis(self): # peak_table = pd.read_pickle('test_peak_table.pkl') p1 = pd.read_pickle('MAmotif_test_input/h1hesc_peak_result.pkl') r1 = pd.read_pickle('MAmotif_test_input/h1hesc_rnd_result.pkl') e1 = pd.read_pickle('MAmotif_test_input/h1hesc_enrich_result.pkl') p2 = pd.read_pickle('MAmotif_test_input/k562_peak_result.pkl') r2 = pd.read_pickle('MAmotif_test_input/k562_rnd_result.pkl') e2 = pd.read_pickle('MAmotif_test_input/k562_enrich_result.pkl') p3 = pd.read_pickle('MAmotif_test_input/common_peak_result.pkl') r3 = pd.read_pickle('MAmotif_test_input/common_rnd_result.pkl') e3 = pd.read_pickle('MAmotif_test_input/common_enrich_result.pkl') [p,r,e] = motifscan_general.merge_two_results(p1,p2,r1,r2,e1) [p,r,e] = motifscan_general.merge_two_results(p,p3,r,r3,e3) core.peak_set_enrichment_analysis(p,'test_fc_plot/')
def test_h_cluster(self): p1 = pd.read_pickle('MAmotif_test_input/h1hesc_peak_result.pkl') r1 = pd.read_pickle('MAmotif_test_input/h1hesc_rnd_result.pkl') e1 = pd.read_pickle('MAmotif_test_input/h1hesc_enrich_result.pkl') p2 = pd.read_pickle('MAmotif_test_input/k562_peak_result.pkl') r2 = pd.read_pickle('MAmotif_test_input/k562_rnd_result.pkl') e2 = pd.read_pickle('MAmotif_test_input/k562_enrich_result.pkl') [p,r,e] = motifscan_general.merge_two_results(p1,p2,r1,r2,e1) core.h_cluster(p,e,'./test_fc_plot',1.3,0.001)
def test_peak_test(self): common_motif_dir = '../MAmotif_H3K4me3_H1hesc_VS_K562/motifscan_on_common_peaks' a_motif_dir = '../MAmotif_H3K4me3_H1hesc_VS_K562/motifscan_on_H1hesc_H3k4me3_Broad_Rep1_P100_unique' print 'Loading motifscan results...' common_peak_result = pd.read_pickle("%s/peak_result.pkl"%common_motif_dir) common_rnd_result = pd.read_pickle("%s/rnd_result.pkl"%common_motif_dir) common_enrich_result = pd.read_pickle("%s/enrich_result.pkl"%common_motif_dir) a_peak_result = pd.read_pickle("%s/peak_result.pkl"%a_motif_dir) a_rnd_result = pd.read_pickle("%s/rnd_result.pkl"%a_motif_dir) print 'Merging peaks...' [positive_peak_result,positive_rnd_result,positive_enrich_result] = \ motifscan_general.merge_two_results(common_peak_result,a_peak_result,common_rnd_result,a_rnd_result,common_enrich_result) core.peak_result_test(positive_peak_result, positive_rnd_result,plot_output_dir='enrichment_plot')