You can try this, since your replacement characters are different for each substitution.

#! /usr/bin/perl

use strict;

my $str='<    <    PU-------------
doc    doc    S-NN-----------
id    id    S-MN-----------
=    =    X--------------
"    "    PU-------------';

$str =~ s/\n//g;
$str =~ s/\s+/\//g;
$str =~ s/(-){2,}/ /g;
print "$str\n";
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