in reply to Re^2: Creating 2 arrays from a larger array
in thread Creating 2 arrays from a larger array

You are in a loop, so $dnaString is being added to everytime the line doesn't match your start pattern. $dnaString is always one step behind @seqList so when you come to the next start line, it pushes the previous $dnaString onto @sequences, then clears it for the next iteration. Best thing to do is try it: set $count = 1 and see what happens.

Update: after re-reading this I'm a bit confused myself. Better to put a print statement within the loop: 
my $dnaString = '';
...
if ($line=~/^>(\S+)/){
    print qq|Count: $count, Match: $1, String: $dnaString\n|;
    push (@seqList, $1);

[download]

Replies are listed 'Best First'.
Re^4: Creating 2 arrays from a larger array
by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 04:08 UTC
    uggg still not getting it. No errors but the elements I printed were all the same. I'll keep working, thanks for explaining!
[reply]
      A HASH makes more sense for this structure: 
      my ($k,$v, %seq);
for my $line (<DATA>) {
  chomp ($line);
  if ( $line=~/^>(\S+)\s*(.*)/){
     $k=$1;
     $v=$2;
  }else{
     $v=$line;
  }
  $seq{$k} .= $v; 
}
#---- Print it ----
for my $k(sort keys %seq){
  print "$k \t=> $seq{$k}\n";
}
# --- Output ---(Using the __DATA__ block above) ..-
#  123     => blahabcdefghijkl
#  456     => de dahmnopqr
#  789     => nothing wanted herestuvwxyz

      [download]

                   All great truths begin as blasphemies.
                         ― George Bernard Shaw, writer, Nobel laureate (1856-1950)

[reply]
[d/l]
      but the elements I printed were all the same
      Can you post some sample data?
[reply]
      Oh it works! It seemed important that the variables were my variables? Thank you soooo much!!
[reply]
Re^4: Creating 2 arrays from a larger array
by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 14:52 UTC
    Yeah here's the file http://www.med.nyu.edu/rcr/rcr/course/smutans.fas
[reply]

In Section Seekers of Perl Wisdom