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.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

In reply to Re^4: remove part of string (DNA) ... More off-topic by BrowserUk
in thread remove part of string (DNA) by Furor

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