# wes_obj = WES() mobem_obj = Mobem() cn_obj = CopyNumber() prot_obj = Proteomics() gexp_obj = GeneExpression() crispr_obj = CRISPR() drug_obj = DrugResponse() # Samples # samples = set.intersection(set(prot_obj.get_data())) LOG.info(f"Samples: {len(samples)}") # Filter data-sets # prot = prot_obj.filter(subset=samples) LOG.info(f"Proteomics: {prot.shape}") gexp = gexp_obj.filter(subset=samples) LOG.info(f"Transcriptomics: {gexp.shape}") crispr = crispr_obj.filter(subset=samples, dtype="merged") LOG.info(f"CRISPR: {crispr.shape}") drespo = drug_obj.filter(subset=samples) drespo = drespo.set_index(
LOG = logging.getLogger("Crispy") RPATH = pkg_resources.resource_filename("reports", "eg/") if __name__ == "__main__": # Data-sets # gexp_obj = GeneExpression() prot_obj = Proteomics() crispr_obj = CRISPR() drespo_obj = DrugResponse() # Samples # samples_crispr = set.intersection( set(prot_obj.get_data()), set(crispr_obj.get_data(dtype="merged")) ) LOG.info(f"CRISPR samples: {len(samples_crispr)}") samples_drug = set.intersection( set(prot_obj.get_data()), set(drespo_obj.get_data()) ) LOG.info(f"Drug samples: {len(samples_drug)}") # Filter data-sets gexp = gexp_obj.filter() LOG.info(f"Gexp: {gexp.shape}") prot = prot_obj.filter() LOG.info(f"Prot: {prot.shape}")