BUGFIX: Filter out N now works with multi-cas files, changes to plotting asthetics in make_pretty_igv

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

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BUGFIX: Filter out N now works with multi-cas files, changes to plotting asthetics in make_pretty_igv #41

Closed allgenesconsidered closed 6 years ago

allgenesconsidered commented 6 years ago

Some bug fixes for gen_sgRNA.py. The way I implemented the filter_out_N_in_PAM() function turned out to be wrong, and filtered out all rows if more than one cas was introduced.

I also didn't implement the 5' PAM notation correctly. It's been tested now with several different cas list and is working.

Also, I implemented the list of available cas enzymes to an option to be displayed, which pulls from the CAS_LIST.txt file.

allgenesconsidered commented 6 years ago

I added another commit for make_pretty_igv.py, which color codes different cas guides. I also added the cas name to the guideID which helps to tell which guides go to which cas for multi cas runs. Let me know what you think, here's a snapshot:

screen shot 2018-05-11 at 12 00 52 pm