Pre-sorting the data seems like good advice to me,

It is quite the opposite of good advice. Ie very bad advice.

1. Sorting is O(N logN). The OPs described processing is O(N).

   Sorting does not help the OPs processing at all.

2. FASTA file are multi-line record format files.

   If you sorted a FASTA file with the system sort utility, it would screw the file up in a completely irrecoverable way.

   Eg. This:

   c:\test>type 845226.fasta
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaacccggccccgcagagccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaaaaaacccggccccgcagagccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaacccggccccgcagagggccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   [download]

   becomes this:

   c:\test>sort 845226.fasta
   >uc002yje.1 chr21:13973492-13976330
   >uc002yje.1 chr21:13973492-13976330
   >uc002yje.1 chr21:13973492-13976330
   acgcgccctacactctggcatgggggaaaaaacccggccccgcagagccctgga
   acgcgccctacactctggcatgggggaacccggccccgcagagccctgga
   acgcgccctacactctggcatgggggaacccggccccgcagagggccctgga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   [download]

   And so is rendered entirely useless.