Why not just do it the simple way, as chomp will remove the '>' (if $INPUT_RECORD_SEPARATOR = '>'), then skip empty records & re-add the '>',
somthing like: 
use English;

local $INPUT_RECORD_SEPARATOR = '>';

while (my $buf = <$fh>) {

       # remove '>' & skip empty records:
       chomp($buf);
       next if ($buf =~ m/^\s*?$/);
       
       my $fasta = ">$buf\n";     

};

[download]

*UPDATE*: added use English;


This is not a Signature...

In reply to Re: Input record separator by monkey_boy
in thread Input record separator by travisbickle34

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