argparse: Argument parsing details
In lawremi/HelloRanges: Introduce *Ranges to bedtools users

argparsing

R Documentation

Argument parsing details

Description

HelloRanges uses docopt for parsing the argument string passed as the cmd argument to functions like bedtools_intersect. bedtools has its own style of argument formatting. Here we document the subtle differences.

Details

Here are the specific differences:

docopt requires that multi-character arguments are prefixed by two hyphens, e.g., --bed. However, bedtools expects only a single hyphen. It turns out docopt is robust to the single-hyphen case, except for the first argument. Since the typical convention is to first indicate the file, e.g., -a or -i, this incompatibility does not often arise in practice.
docopt does not allow values of argument to be space-separated, while bedtools often expects space separation for multi-valued arguments. As a compromise, HelloRanges expects the values to be comma-separated. Thus, -b b.bed c.bed needs to be -b b.bed,c.bed.
Most shells support nested commands within parentheses, e.g., -b < (grep foo file.bed), but docopt does not support that. Instead, nested commands should be enclosed in double quotes, e.g., -b < "grep foo file.bed". Such constructs are supported via pipe.