cossio

Pkg.clone("https://github.com/cossio/Utils.jl")
Pkg.clone("https://github.com/cossio/COBRAUtils.jl")
Pkg.clone("https://github.com/cossio/TruncatedNormal.jl")

cossio

#!/usr/bin/env zsh

submodules=("${(@f)$(find . -type d -depth 1)}")
for submodule in $submodules
do
    print "=== $submodule"
    git --work-tree=$submodule --git-dir=$submodule/.git $*
    print
done

cossio

ENV["JULIA_EDITOR"] = "vim -R"

cossio

pdfimages -j input.pdf output

cossio

"A tensor of zeros"
struct ZeroTensor{T <: Number, N} <: AbstractArray{T,N}
    dims::NTuple{N,Int}
    function ZeroTensor{T,N}(dims::Vararg{Integer,N}) where {T <: Number, N}
        all(dims .≥ 0) || error("invalid ZeroTensor dimensions")
        new(dims)
    end
end
ZeroTensor(T::DataType, dims::Vararg{Integer,N}) where N = ZeroTensor{T,N}(dims...)
ZeroTensor(dims::Vararg{Integer,N}) where {N} = ZeroTensor{Float64,N}(dims...)

cossio

function fib(n::Integer)
  @assert n ≥ 0
  if iszero(n)
    return zero(n)
  elseif n == 1 || n == 2
    return one(n)
  end
  k = div(n,2)
  if iseven(n)
    return fib(k) * (2fib(k+1) - fib(k))

cossio

function dnacompl(nt::Char)
    @assert nt ∈ ('A', 'T', 'C', 'G', 'N', '*')
    if nt == 'A'
        return 'T'
    elseif nt == 'T'
        return 'A'
    elseif nt == 'G'
        return 'C'
    elseif nt == 'C'
        return 'G'

cossio

for i = 1:L, a = 1:A
    @assert sub2ind((A,L),a,i) == (i-1)*A + a
end
for j=1:L, i=1:L, b=1:A, a=1:A
    @assert sub2ind((A,A,L,L),a,b,i,j) == a + (b-1)*A + (i-1)*A*A + (j-1)*A*A*L
end


srand(2);
L = rand(2:10); A = rand(2:10,L);

cossio

function findmaxkey(d::Dict)
    maxk,maxv = first(d)
    for k in keys(d)
        if d[k] > maxv
            maxk, maxv = k, d[k]
        end
    end
    return maxk=>maxv
end

cossio

using Distributions

n = 4969027388018185
p = [4.471459552709845e-5,
0.0021070048390116223,
0.0017485819413324416,
0.0022622153482103544,
0.0019479678673445784,
0.0015864519243622935,
0.00037279832670023585,