use strict;
use warnings;

$/ = ">";

my $fastafile = 'j:\summer\begomo_genomes2.fasta';
my ($OUT, $IN);

print "Input: $fastafile\n";
open my $ifh, "<", $fastafile or die "cannot open $fastafile: $!\n";

while (my $chunk = <$ifh>){
   $chunk = lc $chunk;  
         my ($accession) = $chunk =~ /gi\|(\d+)/;
         my ($acronym) = $chunk =~ /\|\s+(.*),/;
            $acronym =~ s/\[|\]|\:|\d+|\-\///g;
            $acronym =~ s/\s/_/g; 
            $acronym =~ s/dnaa/dna_a/g;
            $acronym =~ s/dnab/dna_b/g;
         my ($sequence) = $chunk =~ /([a|c|t|g]+)\s+/;

   my $outfile = "j:\\summer\\begomo\\${accession}_${acronym}.seq";

open my $ofh, ">", $outfile or die "cannot open $outfile: $!\n";

print "Creating $outfile\n";

print $ofh "$accession $acronym\n^^\n$sequence";

close $ofh;

}