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1 #!/usr/bin/env python
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2 import sys
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3 import argparse
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4 from CPT_GFFParser import gffParse, gffWrite
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5
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6 if __name__ == "__main__":
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7 parser = argparse.ArgumentParser()
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8 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
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9 parser.add_argument("--remark", action="store_true", help="Remove remark features")
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10 parser.add_argument("--region", action="store_true", help="Remove region features")
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11 args = parser.parse_args()
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12
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13 for rec in gffParse(args.gff3):
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14 rec.annotations = {}
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15 if args.remark:
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16 rec.features = [x for x in rec.features if x.type != "remark"]
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17 if args.region:
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18 rec.features = [x for x in rec.features if x.type != "region"]
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19 gffWrite([rec], sys.stdout)
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