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#!/usr/bin/env julia
using ArgParse
using Word2Vec
s = ArgParseSettings()
@add_arg_table s begin
"--model", "-m"
arg_type = String
help = "use this model file (write given -i, query given -q)"
required = true
default = ""
"--input", "-i"
arg_type = String
help = "input text corpus to model"
default = ""
"--kmer-size", "-k"
arg_type = Int
help = "kmer size to break input DNA sequences into"
default = 5
"--kmer-stride", "-s"
arg_type = Int
help = "bases between each successive kmer"
default = 1
"--window-size", "-w"
arg_type = Int
help = "window size to use during word2vec"
default = 30
"--cbow", "-c"
help = "use continuous bag of words in word2vec"
action = :store_true
"--dims", "-d"
arg_type = Int
help = "number of dimensions in embedding"
default = 100
"--query", "-q"
arg_type = String
help = "print the vector for this string"
default = ""
end
parsed_args = parse_args(ARGS, s)
input = parsed_args["input"]
model_file = parsed_args["model"]
model_size = parsed_args["dims"]
query = parsed_args["query"]
kmer_size = parsed_args["kmer-size"]
kmer_stride = parsed_args["kmer-stride"]
window_size = parsed_args["window-size"]
cbow = parsed_args["cbow"]
function kmers_of(k::Int, j::Int, s::String)
[s[i:(i+k-1)] for i in range(1,j,Int(floor((length(s)-k)/j))+1)]
end
function kmers_of_file(k::Int, j::Int, f::String)
kmers = []
for s in readlines(open(f))
append!(kmers, kmers_of(k, j, s))
end
kmers
end
function write_kmers_of(k::Int, j::Int, input::String, output::String)
write(open(output, "w"), join(kmers_of_file(k, j, input), " "))
end
if input != ""
if model_file == ""
println("an output file is required when building a model")
exit(1)
end
kmers = "$input.kmers"
write_kmers_of(kmer_size, kmer_stride, input, kmers)
word2vec(kmers, model_file, verbose = true, size = model_size, window=window_size, cbow=(cbow?1:0))
rm(kmers)
elseif model_file != ""
model = wordvectors(model_file)
if query != ""
kmers = kmers_of(kmer_size, kmer_stride, query)
mean_vec = reduce(+, [(haskey(model.vocab_hash, kmer) ? get_vector(model, kmer) : 0) for kmer in kmers])/length(kmers)
println("$query ", mean_vec)
end
end
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