from conifertools import ConiferPipeline, CallTable, CallFilterTemplate import argparse if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument("conifer_file") parser.add_argument("call_file") parser.add_argument("out_file") args = parser.parse_args() calls = CallTable(args.call_file) p = ConiferPipeline(args.conifer_file) GeneAnnotation = CallFilterTemplate(p, "/net/eichler/vol8/home/nkrumm/REFERENCE_INFO/hg19.refGene.bed", name="RefSeq", filter_type="name") calls = calls.annotate(GeneAnnotation) print_cols = ["cnvrID_SSC", "sampleID", "chromosome", "start", "stop", "state", "size_bp", "cnvr_frequency_SSC", "cohort", "median_svdzrpkm", "num_probes", "RefSeq"] calls.save(args.out_file, cols=print_cols)