Input:

>symbB.v1.2.017277.t1|scaffold1325.1|size176917|3
acggaccgcggcatttgccaatttgcgcgtcgtcgggggtcgccatgatgtttcgcttggcaggcttttttgctttggcactgctggtcgcgggaaagcc caagggtggcaaaggtgcaaaaggagaacaagaccccttctctgagcttagccgcctcgcagacaatttgaaagatgctaaagaacagccggagaaggcc aagaatgctctgaacatgatggatccagaaagtttaggcgattctatggccaacatgatggtgatggcaatggataaggaccaggatggtgtgttgtcag aggaggagattgccaccatggtacaatcgggagagacggagaacaaaggcaaagcagaggagatgtttgaacagatggatgaagatggcgatggagaggt aaccagagacgaagcgaaggtgtacttttcaaaactaggaaacaccttgcaaggcctttcaaaaatgatgggtggttcaaaatcagagttgtgattggga gaatcgctctgtcaaccgcctgcggtggtgcggttggaaggttgagcttgaaaggtgcgaagcgtctctccattggtgtccgagatagcctgagatagcc tgagatatttaggtgatactgtatcttcttgggttttcggatgcaaatttttgacaacagatcagaaatccatccgaatatcccggccgccagggcaaaa atcatagagtttccctgtgcagaagctgcaagttttgagtttttctcattccattggggcctgaatttcaagaaaatcgtatagtctta

Output:

ACGGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA CGGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA GGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA

open ($input, $ARGV[0]) or die ("Could not open input file $ARGV[0].\n
+"); 
open ($output, '>output.txt') or die ("Could not open input file outpu
+t.txt.\n"); 

while ($line = <$input>) { 
 chomp($line);
 unless ($line =~ m/>/) { 
  $line = uc($line);
  $seq .= $line;
  }
 }

$orf1 = $seq;
$orf2 = substr($seq, 1);
$orf3 = substr($seq, 2);
[download]

OK, so the problem is a little different than what I thought earlier. What I'm trying to get is for $seq to be a continuous string of letters, but as you can see, when I use substr it deletes characters on the first line like it should but doesn't shift the other lines (i.e. the GCC on the first line should connect right to the CAA that begins the second line of the output without any spaces or newlines). I'm guessing this is some sort of newline issue? But I used chomp, so I'm confused.