Dear Perl Monks,

I am trying to "hack" (not a real coder)a script to break a text file like this:

>Long_DNA_Scaffold
atgctagsctgtagctagctagtcgatgctagtagct
ttagctagctgatgctagtcgatgctagtcatctagc
NNNNNNNNNNNNNNNNNNN
tagctagctagctgatcgtagctagtcgtagctagct
ggtcgatgctgatcgtagctgatgctagtcgatgcta
>Long_DNA_Scaffold2
atgctagsctgtagctagctagtcgatgctagtagct
tagctagctgatcgtagctagctgatgctagctagtc
NNNNNNNNNNNNNNNNNN
tagctagctagctgatgctagctagtcgatcgtagct
ggctagtgctagtgctagctgatgctagtcgtagctg

Into this:

>Long_DNA_Scaffold.0
atgctagsctgtagctagctagtcgatgctagtagct
ttagctagctgatgctagtcgatgctagtcatctagc
>Long_DNA_Scaffold.1
tagctagctagctgatcgtagctagtcgtagctagct
ggtcgatgctgatcgtagctgatgctagtcgatgcta
>Long_DNA_Scaffold2.0
atgctagsctgtagctagctagtcgatgctagtagct
tagctagctgatcgtagctagctgatgctagctagtc
>Long_DNA_Scaffold2.1
tagctagctagctgatgctagctagtcgatcgtagct
ggctagtgctagtgctagctgatgctagtcgtagctg

This is what a friend and I have tried:
#!/usr/bin/perl -w
open (IN, "$ARGV[0]");
    $/=">";
$i=0;
while (<IN>) {
  if(/^(\S+)?.*?\n(.*)/ms) {
    $i++;
    $seq[$i]=$2;
    $name[$i]=$1;
}
    
}
close IN;
for $j(1..$i){
    $j++;
    tr/>//,$name[$j];
    tr/>//,$seq[$j];
    @sequence=split(/N+/,$seq[$j]);
    
    $n=length(@sequence);
    $seqs_to_print=$n-1;
#    print "$name[$j]\tLength of seqs:$n\n";

    for $x(0..$seqs_to_print){
    print ">$name[$j].$x\n";
    print "$sequence[$x]\n";
    }
}

[download]
It "partially" works and I get a lot of "uninitialized value in transliteration" errors. I will appreciate any help/poiners etc to get it to work

In reply to Seeking help with script by docalf

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