# Review - 09-03-20

Practical 4 notes:
-submission should be a julia script file
-create distance matrix out of practical4.fa or sequences.txt
in file: simulated barcode reads, slight mutations over same sequence - similarity should be high & distance should be low - for this dataset!

[What is a Distance Matrix?](https://www.displayr.com/what-is-a-distance-matrix/)

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Smith-Waterman Visualization
http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Smith-Waterman

Helpful video explanation: https://www.youtube.com/channel/UC8kHK9I5NxHmW0j-RcWQ8cg

Repo to download: https://github.com/mattjones315/LocalAlignment.jl

mkdir <new repo>
#move into new repo
cd <new repo>
module load julia # if on CRC
julia
# adding package from a github repository 
# try to install:
]
add https://github.com/mattjones315/LocalAlignment.jl
# in this case, package was written for a previous version of julia
# if this doesn't work 
# exit julia
git clone https://github.com/mattjones315/LocalAlignment.jl.git
# make sure all files downloaded successfully (compare output of ls to github page)
# read through README to get info regarding use of the package - in this case, run.jl looks like the main file that runs this package
# look through REQUIRE file to see what other packages are needed for this package (aka dependencies)
# add what you don't have 
# see installed packages
]
sort(collect(Pkg.installed()))
ctrl+c
#exit julia and reopen from top directory in repo
include("src/utils/parse.jl")
parse_input("sequences/prot-0004.fa","sequences/prot-0008.fa", "scoring/BLOSUM50")

#output should be a matrix
#assign to a variable 
sw_test = parse_input("sequences/prot-0004.fa","sequences/prot-0008.fa", "scoring/BLOSUM50")
[type] #tupple
sw_test[1] #first sequence
sw_test[2] # second sequence
sw_test[3] # data frame 

# exploration of algorithm in /src/algorithms/smithwaterman.jl - watch class recording to see this code explained
# try algorithm
include("src/algorithms/smithwaterman.jl")
sw_align(sw_test[1],sw_test[2],sw_test[3],5.0,3.0,"output.txt")
# produces error - to figure out what went wrong, explanation of trying individual lines of code 

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## After class

-writing pseudocode:important for week 5 draft code due - https://www.unf.edu/~broggio/cop2221/2221pseu.htm
-julia package creation
package init
https://docs.julialang.org/en/v1/stdlib/Pkg