def preprocess_report(argv=None): p = argparse.ArgumentParser() # input p.add_argument("--illqc-dir", required=True, help="Directory for illqc summary files") p.add_argument("--decontam-dir", required=True, help="Direcrory for decontamination summary files") p.add_argument("--illqc-prefix", default="summary-illqc_", help="Prefix of the illqc summary files") p.add_argument("--decontam-prefix", default="summary-decontam_", help="Prefix of the decontam summary files") # output p.add_argument("--output-fp", required=True, help="Output report file") args = p.parse_args(argv) inputs = [(args.illqc_dir, args.illqc_prefix, ["input", "both_kept", "rev_only", "dropped", "fwd_only"]), (args.decontam_dir, args.decontam_prefix, ["true", "false"])] Report = MergeJson(inputs, args.output_fp) Report.run()
def preprocess_report(argv=None): p=argparse.ArgumentParser() # input p.add_argument("--illqc-dir", required=True, help="Directory for illqc summary files") p.add_argument("--decontam-dir", required=True, help="Direcrory for decontamination summary files") p.add_argument("--illqc-prefix", default="summary-illqc_", help="Prefix of the illqc summary files") p.add_argument("--decontam-prefix", default="summary-decontam_", help="Prefix of the decontam summary files") # output p.add_argument("--output-fp", required=True, help="Output report file") args=p.parse_args(argv) inputs = [ (args.illqc_dir, args.illqc_prefix, ["input", "both_kept", "rev_only", "dropped", "fwd_only"]), (args.decontam_dir, args.decontam_prefix, ["true", "false"]) ] Report = MergeJson(inputs, args.output_fp) Report.run()
def ko_assignment_report(argv=None): p = argparse.ArgumentParser() # input p.add_argument("--pathway-dir", required=True, help="Directory for pathfinder summary files") p.add_argument("--decontam-dir", required=True, help="Direcrory for decontamination summary files") p.add_argument("--pathway-prefix", default="summary-pathway_", help="Prefix of the pathfinder summary files") p.add_argument("--decontam-prefix", default="summary-decontam_", help="Prefix of the decontam summary files") # output p.add_argument("--output-fp", required=True, help="Output report file") args = p.parse_args(argv) inputs = [(args.decontam_dir, args.decontam_prefix, ["false"]), (args.pathway_dir, args.pathway_prefix, [ "ko_hits", "mapped_sequences", "unique_prot_hits", "unique_ko_hits", "mapped_sequences_evalue" ])] Report = MergeJson(inputs, args.output_fp) Report.run()
def ko_assignment_report(argv=None): p=argparse.ArgumentParser() # input p.add_argument("--pathway-dir", required=True, help="Directory for pathfinder summary files") p.add_argument("--decontam-dir", required=True, help="Direcrory for decontamination summary files") p.add_argument("--pathway-prefix", default="summary-pathway_", help="Prefix of the pathfinder summary files") p.add_argument("--decontam-prefix", default="summary-decontam_", help="Prefix of the decontam summary files") # output p.add_argument("--output-fp", required=True, help="Output report file") args=p.parse_args(argv) inputs = [ (args.decontam_dir, args.decontam_prefix, ["false"]), (args.pathway_dir, args.pathway_prefix, ["ko_hits", "mapped_sequences", "unique_prot_hits", "unique_ko_hits", "mapped_sequences_evalue"]) ] Report = MergeJson(inputs, args.output_fp) Report.run()