def transform_to(ext):
    """
    Decorator to create an output filename from an output filename with
    the specified extension. Changes the extension, in_file is transformed
    to a new type.

    Takes functions like this to decorate:
    f(in_file, out_dir=None, out_file=None) or,
    f(in_file=in_file, out_dir=None, out_file=None)

    examples:
    @transform(".bam")
    f("the/input/path/file.sam") ->
        f("the/input/path/file.sam", out_file="the/input/path/file.bam")

    @transform(".bam")
    f("the/input/path/file.sam", out_dir="results") ->
        f("the/input/path/file.sam", out_file="results/file.bam")

    """

    def decor(f):
        @functools.wraps(f)
        def wrapper(*args, **kwargs):
            out_file = kwargs.get("out_file", None)
            if not out_file:
                in_path = kwargs.get("in_file", args[0])
                out_dir = kwargs.get("out_dir", os.path.dirname(in_path))
                safe_mkdir(out_dir)
                out_name = replace_suffix(os.path.basename(in_path), ext)
                out_file = os.path.join(out_dir, out_name)
            kwargs["out_file"] = out_file
            if not file_exists(out_file):
                out_file = f(*args, **kwargs)
            return out_file
        return wrapper
    return decor
def transform_to ( ext ) : def decor ( f ) : @ functools . wraps ( f ) def wrapper ( * args , ** kwargs ) : out_file = kwargs . get ( "out_file" , None ) if not out_file : in_path = kwargs . get ( "in_file" , args [ 0 ] ) out_dir = kwargs . get ( "out_dir" , os . path . dirname ( in_path ) ) safe_mkdir ( out_dir ) out_name = replace_suffix ( os . path . basename ( in_path ) , ext ) out_file = os . path . join ( out_dir , out_name ) kwargs [ "out_file" ] = out_file if not file_exists ( out_file ) : out_file = f ( * args , ** kwargs ) return out_file return wrapper return decor
Decorator to create an output filename from an output filename with
    the specified extension. Changes the extension, in_file is transformed
    to a new type.

    Takes functions like this to decorate:
    f(in_file, out_dir=None, out_file=None) or,
    f(in_file=in_file, out_dir=None, out_file=None)

    examples:
    @transform(".bam")
    f("the/input/path/file.sam") ->
        f("the/input/path/file.sam", out_file="the/input/path/file.bam")

    @transform(".bam")
    f("the/input/path/file.sam", out_dir="results") ->
        f("the/input/path/file.sam", out_file="results/file.bam")