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)
