To save yourself some grief, I would simply look for > and then replace the line, regardless of what else is there (which is what you are doing anyway). You can also use print $variable and sleep(3); in parts of the code to help see what is present in certain places, particularly if you don't get a match. We don't have the input files, so we can't tell if there are spaces or tabs in the FASTA headers.
use strict;
use warnings;
my @files = glob("*.fa");
for my $file ( @files ) {
# open the input file
open my $in, "<", "$file" or die "Cannot open "$file": $!\n";
# open the output file
open my $out, ">", "$file.out" or die "Cannot open "$file.out": $!\
+n";
# reset contig number
my $contig_number = 1;
while ( <$in> ) {
chomp;
if ( $_ ~= m/^>/ ) {
# it's a header
print $out ">config_$contig_number\n\n";
$contig_number++;
}
else {
# it's sequence
print $out "$_\n\n";
}
close $in;
close $out;
}
}
my $file_count = @files;
print "Successfully processed $file_count files!\n";
exit;