#make an array [["chrN", start, expression]]
def profile_array(array, lines)
    lines.each do |line|
        line = line.split()
        chr = line[0]
        start = line[1].to_i
        expression = line[4].to_i
        array.push([chr, start, expression])
    end
    return array
end

#make an array of peaks segments[["chrN", start of segment, end of segment]]
def array_of_peaks(arr, lines)
    lines.each do |line|
        chr = line.split(":")[0]
        start = (line.split(":")[1].split("..")[0]).to_i
        fin = (line.split(":")[1].split("..")[1].split(",")[0]).to_i
        arr.push([chr, start, fin])
    end
    return arr
end

#take lines that correspond to certain chr
def choose_chr(profile, profile_chr)
    profile.each do |el|
        if el[0] == "chr1"
            profile_chr.push(el)
        end
    end
    return profile_chr
end

#make an array with array[index] = 0 if index doesn't lie in segment
#start and fin - places where chr "starts" and "ends" respectively
#for chr1 start = 564473, end = 249214301
def make_chr_array(profile_chr, start, fin)
    indexed_profile = Array.new(start - 1) {0}
    for index in start...fin
        profile_chr.each do |el|
            if index == el[1]
                indexed_profile.push(el[2])
            else
                indexed_profile.push(0)
            end
        end
    end
    return indexed_profile
end


file = File.open('file', 'r')
lines = file.readlines()