This week I got an introduction to Vi (learned about command mode and navigation) and I started coding in vi. Since vi is on every unix server, its good to have at least a basic understanding of how to use it. However, there was a steep learning curve to using vi and I had to keep looking at a cheat sheet I made for how to navigate around and do basic things like copying and pasting. It took a lot longer for me to code simple things at the beginning of the week, but by the end of the week it got a lot better. At the beginning of the week the first thing I did was make sure to back up all of my notes and the shell scripts I had generated so far, since I had finally gotten a working version of my VCF to 23&Me converter. I created a script to run on all my 23&Me files to confirm that there were no strange lines in the data files. The process of creating this script took several iterations as I found different things in some of the files that I had to confirm were valid or not. This week we also talked about wildcards in the shell, shell variables and date, as well as when to use single or double quotes in the shell. We also talked about SQL and relational databases and I practiced using sqlite3 to insert, delete and update entries in a practice database and learning how to create databases and tables. I started working on a python script that takes a 23&Me file and a dbSNP version and checks to make sure every line of the 23&Me file is in that version of dbSNP. I set up sqlite3 databases corresponding to the latest dbSNP versions for various builds of the genome.