
Reading DNA and Count Bases in Raku – Suman Khanal - lizmat
https://sumankhanal.netlify.app/post/raku/count_dna/
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dalke
I wrote bioinformatics software a long time ago. Meaning that I remember
reading the bioperl code back to read FASTA files around Y2K.

Their technique is still in use, at [https://github.com/bioperl/bioperl-
live/blob/master/lib/Bio/...](https://github.com/bioperl/bioperl-
live/blob/master/lib/Bio/SeqIO/fasta.pm) . The key point is they set the input
record separator, like this:

    
    
        local $/ = "\n>";
    

This gets Perl to read each FASTA record as a single block, which they then
post-process into title and sequence.

Raku has a per-filehandle version, according to
[https://docs.raku.org/language/5to6-perlvar](https://docs.raku.org/language/5to6-perlvar)

In principle, since it does more work closer to the machine, it should be
faster. I haven't tested it.

