>scaffold00001
TGACCAGCGTTACATGTCAACGTTTTTTTAAACATTGAATATTTATTCATCTGTTCTCGA
CGTCGCACATTGTGCAAGCCATCAACTTGATCTAATTAAGTATATCCGCTAAAGATCAGC
GCCTTTTGTTTTGACAACAACAAGTATCATACCAGCACTTTAACGATGTAGTCAATAAAA
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
TGTCTGCTTCCGTTGATACCTGCGCGAGCCGGTCGTCACGATTCGGTACCTTGCCGTCAA
TCAAAAAATGGCAATGATGATCCAACAATGGGACTTGGTCGACAAACTCAGATAAGTCGT
CCAAAATACTTCCTCCTTCACACGTTTGCTGGTGCAATGACCAGCCCACGTTTTCCTAGA
>scaffold00002
ATTCATGTTGCTCGTCGTCACCTGACCGAGCAGGGCCAGAACCGGGACATGATCCATTTT
GGCATCATACAAACCATTTAATAGATGAATGGCGCCAGGGCCGCCAATGGAGAGACAAAC
ACCCAAACCGCCTGTTAACTTAGCAGTTGCCGCTGCGGACAAAGCGGCGACTTCCTCATG
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
CAACTGCTCTTAGTGTGATCTCATTTATCAAAGAGATCAGACTTTGTGAATTCAGATTTT
TTCAAGCCATACAACAACTAACCCAATTTAAGAAATACCCACTTATTGCGATTTGCTTTT
CTATTAGTTAGCATTTTAAATTGTGAAACGTGCCACTTATAAACAAATTTCCGTCTTCTT

##</code><code>##


#!/util/bin/perl
use strict;
use warnings;
use File::Copy;
#################


#-----Declaration of Arguements-----#

my $fasta=$ARGV[0] || die ("Please provide a 454Scaffolds.fna fasta file to parse.\n"); # Argument accepts scaffold fasta file.
my $tempfasta="temp.fasta";
my $workingfasta="working.fasta";
my $scaffold;                                                                           # Initializing $scaffold globally.
my $enumerator;                                                                         # Initializing $enumerator globally.

#----Main Program-----#

copy($fasta, $tempfasta) or die "Could not copy $fasta to $workingfasta.";



open (FILE,"<temp.fasta") || die ("Could not open fasta file!\n"); # Open & read fasta file
open (WORKFILE,">>working.fasta");
while (my $fastaline=<FILE>)
  {
    if($fastaline=~ m/^>/)                                             # IF first character in line is > assign line to $fastaline then...
    {
    my $scaffold_header=$fastaline;                                     # set $scaffold_header to $fastaline then... 
    $scaffold_header=~ /(>)(\S*)(\s*)(\S*)/;                            # divide $ scaffold header components then...
    $scaffold= $2;                                                      # assign component $2 to $scaffold then...
    print WORKFILE ">" . "$scaffold" . ".1\n";                          # print $scaffold to screen and start new line.
    $enumerator=1;
}  elsif ($fastaline!~ m/G/ and $fastaline!~ m/A/ and $fastaline!~ m/T/ and $fastaline!~ m/C/) 
  {
  $enumerator++; 
  print WORKFILE (">" . "$scaffold" .  ".$enumerator\n");  
} else {
  print WORKFILE $fastaline;
}
};
close (FILE);
close (WORKFILE);

##</code><code>##

>scaffold00001.1
TGACCAGCGTTACATGTCAACGTTTTTTTAAACATTGAATATTTATTCATCTGTTCTCGA
CGTCGCACATTGTGCAAGCCATCAACTTGATCTAATTAAGTATATCCGCTAAAGATCAGC
GCCTTTTGTTTTGACAACAACAAGTATCATACCAGCACTTTAACGATGTAGTCAATAAAA
>scaffold00001.2
>scaffold00001.3
>scaffold00001.4
TGTCTGCTTCCGTTGATACCTGCGCGAGCCGGTCGTCACGATTCGGTACCTTGCCGTCAA
TCAAAAAATGGCAATGATGATCCAACAATGGGACTTGGTCGACAAACTCAGATAAGTCGT
CCAAAATACTTCCTCCTTCACACGTTTGCTGGTGCAATGACCAGCCCACGTTTTCCTAGA
>scaffold00002.1
ATTCATGTTGCTCGTCGTCACCTGACCGAGCAGGGCCAGAACCGGGACATGATCCATTTT
GGCATCATACAAACCATTTAATAGATGAATGGCGCCAGGGCCGCCAATGGAGAGACAAAC
ACCCAAACCGCCTGTTAACTTAGCAGTTGCCGCTGCGGACAAAGCGGCGACTTCCTCATG
>scaffold00002.2
>scaffold00002.3
CAACTGCTCTTAGTGTGATCTCATTTATCAAAGAGATCAGACTTTGTGAATTCAGATTTT
TTCAAGCCATACAACAACTAACCCAATTTAAGAAATACCCACTTATTGCGATTTGCTTTT
CTATTAGTTAGCATTTTAAATTGTGAAACGTGCCACTTATAAACAAATTTCCGTCTTCTT

##</code><code>##

>scaffold00001.1
TGACCAGCGTTACATGTCAACGTTTTTTTAAACATTGAATATTTATTCATCTGTTCTCGA
CGTCGCACATTGTGCAAGCCATCAACTTGATCTAATTAAGTATATCCGCTAAAGATCAGC
GCCTTTTGTTTTGACAACAACAAGTATCATACCAGCACTTTAACGATGTAGTCAATAAAA
>scaffold00001.2
TGTCTGCTTCCGTTGATACCTGCGCGAGCCGGTCGTCACGATTCGGTACCTTGCCGTCAA
TCAAAAAATGGCAATGATGATCCAACAATGGGACTTGGTCGACAAACTCAGATAAGTCGT
CCAAAATACTTCCTCCTTCACACGTTTGCTGGTGCAATGACCAGCCCACGTTTTCCTAGA
>scaffold00002.1
ATTCATGTTGCTCGTCGTCACCTGACCGAGCAGGGCCAGAACCGGGACATGATCCATTTT
GGCATCATACAAACCATTTAATAGATGAATGGCGCCAGGGCCGCCAATGGAGAGACAAAC
ACCCAAACCGCCTGTTAACTTAGCAGTTGCCGCTGCGGACAAAGCGGCGACTTCCTCATG
>scaffold00002.2
CAACTGCTCTTAGTGTGATCTCATTTATCAAAGAGATCAGACTTTGTGAATTCAGATTTT
TTCAAGCCATACAACAACTAACCCAATTTAAGAAATACCCACTTATTGCGATTTGCTTTT
CTATTAGTTAGCATTTTAAATTGTGAAACGTGCCACTTATAAACAAATTTCCGTCTTCTT

##</code><code>##

 elsif ($fastaline!~ m/G/ and $fastaline!~ m/A/ and $fastaline!~ m/T/ and $fastaline!~ m/C/)