Determining variant repeat length of Myotonic Dystrophy type 1 patient from raw sequences

Notable project files:

• optimisations.txt lists all attempted changes/optimisations (description, test, reasoning...)
• pyth_orig/ contains the original python implementation from https://github.com/picrin/science_of_alignment/blob/master/variant_repeat_algorithm.ipynb
• scorecode/ contains the align scoring code. compilation: ./compile.sh
• scorevisualizers contains visualizers for outputs of align scoring code (distribution of results per parameter, param vs. param etc.) ^ use python3 somevisualizer.py to get usage, -h for list of options
• sequences/ contains sample DNA sequences (real.txt is parsed from github, garbagefree.txt after trimming. raw/ contain the original raw data) ^ due to privacy, they are not part of the repo. Raw data is on S3 in dm1data bucket.
• test/ contains output of testing different optimisations
• outputs/ contains data-outputs
• windowcode, windowvisualizers is a similar pair for an (un)supervised sliding window approach
• HMM contains code for the Hidden Markov Model approach
• Tablet contains files used for visualization of our data in Tablet (early work in progress)

All tests were done on a single core of a intel i7-5500U CPU @ 2.40GHz