lines such as
%head_seqs = @headers_seqs;
make no sense.

It makes perfect sense.    Copying values between lists, arrays and hashes is a normal idiom in Perl. 

            if ($line =~ /$key/)
            {
                $line =~ s/$key/$headers{$key}/;
                last;
            }

[download]

Your $key values may contain regular expression meta-characters so you should use quotemeta on them.

Your loop exits on the first match but not necessarily the correct match.    You should anchor the patterns.

In reply to Re^2: replace FASTA sequence headers by jwkrahn
in thread replace FASTA sequence headers by onlyIDleft

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