Find the complement set of an array?

Ok, on second thought - I worked way too hard on that. You just need this:

shuf -i 1-100 -n10 |
sed 's/$/{p;b\n}/' |
sed -nf - -e 'w separate_file' infile >outfile

Though you might need a literal newline in-place of the n in the sed substitution. Anyway that does the same as below - it just doesn't bother doing all of the other 90 lines - they just fall into place because they're in the file - so they don't need any special consideration.

Here's the whole deal:

set  " $(shuf -i 1-100 -n 10) "
while [ "$((i+=1))" -le 100 ]
do    [ -z "${1##*[!0-9]$i[!0-9]*}" ]
      printf "$i%.$((!$?))s%.$?s\n" p H 
done| sed -nf - -e '$!d;x;s/.//p' <infile >outfile

There - we just basically write a sed script that looks like:

1H
2H
3H
4p
5H
...
90p
91H
...

And so on through to 100. On the last line - after all of the randomly selected lines have already been printed, we exchange into Hold space, s///ubstitute away the first inserted \newline character, and print the lot of the rest.

To do this without the shell loop you could do:

set  "$(shuf -i 1-100 -n 10)"
{ seq 100 | grep -Fxv "$1"; echo "$1"; } |
sed '1,90s/$/H/;91,$s/$/p/' |
sed -nf - -e '$!d;x;s/.//p' <infile >outfile

But I'm not sure whether on this scale that would be beneficial at all.

Anyway, I used a seq 100 output file as a test, and after running it through it printed...

3
4
5
19
57
63
64
73
80
88
1
2
6
7
8
9
10
11
12
13
14
15
16
...

...and on through to 100 for all of the lines not included in the initial random 100.

I believe you can do everything on the command line, but some problems are better solved with an actual programming language. As an example, a python based solution to your problem would be:

import random
import pprint

with open("file.txt", "w") as f:
  # create a file filled with numbers from 00 to 99
  f.writelines(map(lambda x: "%02d\n" % x, range(100)))

with open("file.txt") as f:
  # read it and assign each line to array, strip newlines 
  ar = set(map(lambda x: x.strip(), f.readlines()))

selection = set(random.sample(ar, 10))
rest = ar - selection

pprint.pprint(selection)
pprint.pprint(rest)