#
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}")