see perlvar

$LIST_SEPARATOR
$"
When an array or an array slice is interpolated into a double-quoted string or a similar context such as /.../ , its elements are separated by this value. Default is a space. For example, this:
    print "The array is: @array\n";
is equivalent to this:
    print "The array is: " . join($", @array) . "\n";

Either use

{
  local $" = '';
  print FH "@fasta";
}
[download]

or

print FH join '',@fasta;

or just print out each line as it is read

#!/usr/local/bin/perl 
use strict;
use Text::CSV;
use Data::Dumper qw(Dumper);

print "Enter input file name : ";
my $file = <STDIN>;
chomp $file;
open my $in, '<', $file 
   or die "Could not open '$file' $!\n";

print "Enter output file name: ";
my $ofile = <STDIN>;
chomp $ofile;
open my $out, '>', $ofile 
   or die "Could not open '$ofile' $!\n";   
   
my $csv = Text::CSV->new({ sep_char => ',' });
my $count = 0; 
while (my $line = <$in>) {
  if ($csv->parse($line)) {
     my @fields = $csv->fields();
     $fields[4]=~s/\s//g; #removes spaces within the sequence
     print $out '>'.(join '_',@fields[0..3])."\n$fields[4]\n";
  } else {
     warn "Line could not be parsed: $line\n";
  }
  ++$count;
}
close $in;
close $out;
print "$count lines read from $file to $ofile\n";
[download]

poj