[Tutor] R: Tutor Digest, Vol 138, Issue 26 Re: Problem on select esecution of object in a class (Alan Gauld)
steve at pearwood.info
Mon Aug 10 05:15:15 CEST 2015
I'm not sure if you have received an answer to your question.
It might help if you use a subject line that describes your question.
See below for my answer:
On Wed, Aug 05, 2015 at 10:33:01PM +0200, jarod_v6--- via Tutor wrote:
> Thanks so much fro the help. What I want to do is to obtain a selection of the
> function I want to run.
> ena = Rnaseq(options.configura, options.rst, options.outdir)
> cmdset = [ ena.trimmomatic,
> 1 ena.trimmomatic
> 2 ena.star
> 3 ena.merge_trimmomatic_stats
> The class RNaseq have multiple function. I want a way to run or from 1 to 3 or
> from 2 to 3 or only the 2 o 3 step.
> parser.add_option("-s", "--step",action="store", dest="steps",type="string",
> help=" write input file: %prg -o : directory of results ")
> python myscript -s 1,3 ...
> At the moment the only way I found is this:
> for cmd in cmdset:
> step = cmd()
> for i in step:
> print i.command
> but is not elegant so I want to know more what is the right way to generate a
> execution f the function of the class by select which is the step we want to
This is hard to answer since you don't tell us directly what cmdset is,
but I think I can guess. Something similar to this should work:
cmdset = ena.cmdset
options = "1,3" # for example
options = options.replace(",", " ").split()
# options now has ["1", "3"]
options = [int(s) for s in options]
# options now has [1, 3], integers, not strings
for opt in options:
cmd = cmdset[i-1] # remember Python starts counting at 0, not 1
Does that help?
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