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()
