use warnings FATAL => 'all';
use strict;


my %hash = (
    'nc7-52' => 'C_fraterna',
    'mi9-87' => 'D_whatever',
    );

my ($search) =
    map  qr{ $_ }xms,
    join ' | ',
    keys %hash
    ;
print "search regex: \n", $search, "\n\n";  # FOR DEBUG


print "output: \n";
while (<DATA>) {
    my $line = $_;
    $line =~ s{ \A ($search) (?= :) }{$hash{$1}_$1}xms;
    print $line;
    }


__DATA__
nc7-52:p39|read1|1|19|296|0.0642
ia1-23:p42|read1|1|19|296|0.0642
mi9-87:p77|read1|1|19|296|0.0642