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keoughkath / AlleleAnalyzer

A software tool for personalized and allele-specific CRISPR editing.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1783-3
MIT License
16 stars 5 forks source link

Small change to get_chr_table, made complete python version. #9

Closed allgenesconsidered closed 6 years ago

allgenesconsidered commented 6 years ago

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

PS I made a pull request earlier, but I originally forgot line 113 which removes the temp file.

keoughkath commented 6 years ago

Hi Michael,

Thanks for the suggestions. I'm going to wait on merging this pull request until you have a chance to go through the new stuff because I want to make sure the changes will integrate. Overall all of these ideas are great though.

Cheers, Kathleen

keoughkath commented 6 years ago

Merged - thanks!