I'm taking a look at the changes you've made to ExcisionFinder as a whole, however while I've been looking over them I thought about 'get_chr_tables.sh'. If there's still interest in making a CLI, I think it would be best to have everything written in python.
I've rewritten the gen chr scripts into one file called 'get_chr_tables.py', using the subprocess module. I've checked the outputs and everything seems to be working. I don't have any experience with docopt, so if you could check that I've implemented everything correctly that would be good.
If we choose not to go this route, the only thing I ask is that we start making calls to python3 explicitly, since most OS's still come with python2 as the default, and a call to python usually invokes python2.
Hi Kathleen,
I'm taking a look at the changes you've made to ExcisionFinder as a whole, however while I've been looking over them I thought about 'get_chr_tables.sh'. If there's still interest in making a CLI, I think it would be best to have everything written in python.
I've rewritten the gen chr scripts into one file called 'get_chr_tables.py', using the subprocess module. I've checked the outputs and everything seems to be working. I don't have any experience with docopt, so if you could check that I've implemented everything correctly that would be good.
If we choose not to go this route, the only thing I ask is that we start making calls to python3 explicitly, since most OS's still come with python2 as the default, and a call to python usually invokes python2.
Best, Michael