I cannot understand this sentence: 
if (($head =~ /$_/) .. ($_ =~ /\/\//))

[download]
What are you doing here?

In fact, the most sensible way to do your job is to load the FASTA sequence file into a hash: 
my %fasta_source;

my $tmp_title;
open INSEQ,"<$file_fasta";
while (<INSEQ>) {
    chomp;
    if ($_=~/^>/) {
        $tmp_title=$_;
    }
    else {
        $fasta_source{$tmp_title}.=$_;
    }
}
close INSEQ;

[download]
This should put the FASTA file into the hash "fasta_source", and you would easy to do what you want.

In reply to Re: One more problem by llancet
in thread While loop printing only one fasta header file by ashnator

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