How to use the cutadapt.adapters.warn_duplicate_adapters function in cutadapt

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github marcelm / cutadapt / src / cutadapt / __main__.py View on Github external
def adapters_from_args(args) -> Tuple[List[Adapter], List[Adapter]]:
    adapter_parser = AdapterParser(
        max_error_rate=args.error_rate,
        min_overlap=args.overlap,
        read_wildcards=args.match_read_wildcards,
        adapter_wildcards=args.match_adapter_wildcards,
        indels=args.indels,
    )
    try:
        adapters = adapter_parser.parse_multi(args.adapters)
        adapters2 = adapter_parser.parse_multi(args.adapters2)
    except (FileNotFoundError, ValueError) as e:
        raise CommandLineError(e)
    warn_duplicate_adapters(adapters)
    warn_duplicate_adapters(adapters2)
    if args.debug == "trace":
        for adapter in adapters + adapters2:
            adapter.enable_debug()
    return adapters, adapters2
github marcelm / cutadapt / src / cutadapt / __main__.py View on Github external
def adapters_from_args(args) -> Tuple[List[Adapter], List[Adapter]]:
    adapter_parser = AdapterParser(
        max_error_rate=args.error_rate,
        min_overlap=args.overlap,
        read_wildcards=args.match_read_wildcards,
        adapter_wildcards=args.match_adapter_wildcards,
        indels=args.indels,
    )
    try:
        adapters = adapter_parser.parse_multi(args.adapters)
        adapters2 = adapter_parser.parse_multi(args.adapters2)
    except (FileNotFoundError, ValueError) as e:
        raise CommandLineError(e)
    warn_duplicate_adapters(adapters)
    warn_duplicate_adapters(adapters2)
    if args.debug == "trace":
        for adapter in adapters + adapters2:
            adapter.enable_debug()
    return adapters, adapters2