Easy.

Put the sequences in an array, shuffle the array and then take the first 1000 elements.

use Modern::Perl;
use List::Util qw/shuffle/;

my @sequences = (shuffle <DATA>)[0 .. 9];
chomp @sequences;
say "@sequences"

__DATA__
first
second
third
fourth
fifth
sixth
seventh
eight
ninth
tenth
eleventh
twelveth
thirteenth
fourteenth
fifteenth
sixteenth
seventeenth
eighteenth
nineteenth
twentieth

[download]
Or, taking advantage of the pseudo-random order of the hash-keys:
my %sequences = map {chomp; $_ => 1} <DATA>;
my @sequences = (keys %sequences)[0 ..9];
say "@sequences";

[download]

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

In reply to Re: Extract subset of sequences from a FASTA file by CountZero
in thread Extract subset of sequences from a FASTA file by silver_steve

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