mutation count

[necrolyte2]

Inputs

• Reference base sequence(Single sequence)
• Reference set(Multiple sequences)
• Query set(Multiple sequences)

Output

• 2D axis
  • X axis being time(years since reference sequence date)
  • Y mutation count from reference base sequence
  • Reference sequences would need to be easily distinguished from query set
  • Maybe mark the standard deviation along the graphic and/or highlight sequences that fall outside of this

The goal here is to be able to easily pick out sequences from the Query set that fall outside of the expected mutation count.

I believe the way to achieve this is going to be something like:

1. to align each reference sequence against the base reference and plot them.
2. Then align each query sequence against the base reference and plot them
3. Somehow highlight the points that fall outside of STDDEV of the reference set

@InaMBerry
@mmelendrez
@averagehat

A project I started 2 years ago does some of this already and we can use it as a base or just completely rewrite the whole thing https://github.com/VDBWRAIR/MutationCount

In that project you can see in the sample_data directory there are 2 directories. H3N2 and H1N1 which are two example sets that were run.
In each of them is a README that explains how the files were generated.
Essentially, you end up with a tab file that contains 2 columns

Column 1 represents the sequence name
Column 2 represents the number of mutations from the reference

[necrolyte2]

Closed in #70