file = "Data/GSE42308.txt"
samples = Core.ParseFile(file).get_samples()
# samples2 = Core.ParseBatch("Data/").get_all_samples()
probes = annotations.get_probes(annotations.get_all_probe_ids())
print(len(probes))
probe2 = Annotation.get_probes_from_feature(probes, Annotation.Feature(Annotation.CpG_location.ISLAND))
print(len(probe2))
probe3 = Annotation.get_probes_from_feature(probe2, Annotation.Feature("BRCA1"))
print(len(probe3))
brcaprobes = annotations.get_probes(annotations.get_probes_id_from_gene("BRCA1"))
#groups= [groups[0], groups[3]]
Plot.BoxPlot(probes, samples)
# probe_list = annotations.get_probes_from_gene("TP53")
# probe_list2 =annotations.get_probes_id_from_loc(Annotation.Location.BODY)
# probe_list3 =annotations.get_probes_id_from_cpg(Annotation.CpG_location.NSHORE)
# print(probe_list3)
# sort data
# probe_list = annotations.sort_coord_probe(probe_list)
# Core.write_data("data.txt", groups, probe_list)
Plot.Heatmap(samples, brcaprobes, "brca1.png")
