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• Commented on FASTA splitter
  If BioPerl6 becomes a thing, I won't mind at all :)...
• Commented on The sad story of pseudohash criticism
  Maybe someday the extent of your feigned respect will even go so far that you'll bother to spell his fucking name right....
• Commented on Inline::C optimizations
  I'd go even a step further on the pure-perl route. Lose the state machine, lose "ord", lose the conditional. Build a table of codes and what they generate, and put it in a hash. Do my $codes_regex = join '|',...
• Commented on Grepping exact values
  Combinining Nilson's and Sawyer's observations: if you're only testing for existence of a fixed string or number -- there's no need to return the values, since you already know what they are, and it's only rarely that you're looking for...

Comment Threads

• Ken Youens-Clark commented on FASTA splitter

  BioPerl6 is a thing and a very good thing it is (https://github.com/cjfields/bioperl6). Sorry, I should have mentioned that I could have used their FASTA parser. Here I wanted to present a self-contained script for purposes of exploring just a couple of ideas.

• Pawel bbkr Pabian commented on FASTA splitter

  Thanks for sharing your knowledge. I've learned about $*SPEC from your post :)

  I'm not FASTA expert, but my approach would be to use ">" as input separator instead of "\n". And then simply push 100 lines (=sequences) into each file through rotor:

  # beware first empty element
  writer($_) for $fasta.IO.lines( nl-in => '>').[1..*].rotor(100, :partial);

  sub writer (@seqs) {
  ...
  # restore sequence start character
  $out.print('>', $_); for $seqs;
  };

  Of course TIMTOWTDI, however - from my experience - delimiter approach is waaa…

• Pawel bbkr Pabian commented on FASTA splitter

  My mistake, should be:

  $out.print('>', $_); for @seqs;

• Ken Youens-Clark commented on FASTA splitter

  Sorry, there's a bug in there in that I didn't re-incorporate the newlines from the original sequences. How embarrassing. Here's a corrected version:

  #!/usr/bin/env perl6
  
  sub MAIN (
  
      Str :$fasta! where *.IO.f,
  
      Int :$number=100,
  
      Str :$out-dir=$*PROGRAM.IO.d
  
  ) {
  
      mkdir $out-dir unless $out-dir.IO.d;
  
      my $ext      = $fasta.IO.extension;
  
      my $basename = $fasta.IO.basename;
  
      $basename ~~ s/\.$ext$//;
  
      sub writer (@seqs) {
  
          state $fnum = 0;
  
          my $fname = $*SPEC.catfile(
  

• Ken Youens-Clark commented on FASTA splitter

  Nice use of "rotor" and "nl-in" to shorten up the code, Pawel! Here's a new version that I like much better using those ideas:

  #!/usr/bin/env perl6
  
  sub MAIN (
  
      Str :$fasta! where *.IO.f,
  
      Int :$number=100,
  
      Str :$out-dir=$*PROGRAM.IO.d
  
  ) {
  
      mkdir $out-dir unless $out-dir.IO.d;
  
      my $ext   = $fasta.IO.extension;
  
      (my $base = $fasta.IO.basename) ~~ s/\.$ext$//;
  
      my $fh    = open $fasta, :r, nl-in => '>';
  
      my $fnum  = 0;
  
      for $fh.lines.[1..*].rotor($number, :partial) -> @seqs {
  
       …