x1 = []; y1 = []; x2 = []; y2 = []; z = []
i = 0; k = -1
filename = "File1"

File.open(filename) do |file|
file.each_line do |line|
if line.start_with?("No.")
k += 1
else
x1[i] ||= []; y1[i] ||= []; x2[i] ||= []; y2[i] ||= []; z[i] ||= [];
x1[i][k], y1[i][k], x2[i][k], y2[i][k], z[i][k] = line.split()
i += 1
end
end
end

p x1, y1, x2, y2, z

Ruby で書いた。出力は、

[["1"], ["2"], [nil, "1"], [nil, "2"], [nil, "3"], [nil, nil, "3"]]
[["2"], ["3"], [nil, "2"], [nil, "2"], [nil, "3"], [nil, nil, "4"]]
[["3"], ["4"], [nil, "3"], [nil, "2"], [nil, "3"], [nil, nil, "5"]]
[["4"], ["5"], [nil, "4"], [nil, "2"], [nil, "3"], [nil, nil, "6"]]
[["5"], ["6"], [nil, "5"], [nil, "2"], [nil, "3"], [nil, nil, "7"]]

https://paiza.io/projects/LKdkdq3Lqgu5cw_MTOTBYA