[Tutor] R: Tutor Digest, Vol 138, Issue 26 Re: Problem on select esecution of object in a class (Alan Gauld)

Alan Gauld alan.gauld at btinternet.com
Mon Aug 10 10:12:27 CEST 2015

On 05/08/15 21:33, jarod_v6--- via Tutor wrote:

> ena = Rnaseq(options.configura, options.rst, options.outdir)
> 		cmdset = [ ena.trimmomatic,
> 					ena.star,
> 					ena.merge_trimmomatic_stats

Steven has shown you one option using a list.
I tend to prefer dictionaries for this kind of thing because
you can use a user-friendly key. So your cmdset might look like:

cmdset = { 'trim': ena.trimmomatic,
            'star': ena.star,
            'merge': ena.merge_trimmomatic_stats

You can then create a menu using the keys:

for key in cmdset: print(key)
cmd = input('command? ')

And call the command with


If the commands have different parameter requirements
you might need a helper function to gather those params
too - it can also be in the dictionary:

cmdset = { 'trim': [ena.trimmomatic, get_trim_par],
            'star': [ena.star, get_star_par],
            'merge': [ena.merge_trimmomatic_stats, None]

So calling now becomes

if cmdset[cmd][1]:

And that can be put into a loop for multiple steps:

for cmd in steps:
    if cmdset[cmd[[1]: etc...

If you need to get the steps from the command line
then you need to adapt that pattern to gather the
params in another way - possibly via a data file
(which could also be specified on the command line)
or by using defaults.

Alan G
Author of the Learn to Program web site
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