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  • Perl: get specific base from FASTA file.

    I've written a piece of Perl code that retrieves a base from a FASTA file, given the contig label (e.g. chr1) and base position. However- I think it runs slowly, and am sure is not optimal: mainly because requests are usually made in an ordered manner, which is not reflected by my code.

    Is anyone aware of a function that has already been written to do this well?

  • #2
    samtools faidx /path/to/your/genome.fa chr1:base_position

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    • #3
      Fast response- thanks

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      • #4
        No problem. I was just incorporating that little bit into one of my perl scripts yesterday. Glad it could help.

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        • #5
          FYI:
          using Benchmark:

          Rate mine samtools
          mine 111/s -- -92%
          samtools 1449/s 1201% --

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          • #6
            Are you using Bio:: DB ::Fasta? (Apologies for the spaces; otherwise the I get a smilie version: Bio:B::Fasta)

            For your benchmark, are you calling samtools repeatedly or once? If you have multiple requests, better to batch them up and call samtools -- there's an overhead in process creation and probably in firing up samtools.

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            • #7
              Thanks. No, I'm not- but I'll take a look.

              Not sure how you would go about bundling these requests, is it possible to pass samtools an array of positions, returning a corresponding array of bases?

              Benchmarking calls the following function X times.

              Currently looks something like:

              sub getFASTABaseSamtools
              {
              my $chrID = shift;
              my $basepos = shift;
              my $fastapath = shift;
              my @result = `samtools faidx $fastapath $chrID:$basepos-$basepos`;
              chomp($result[1]);
              return uc($result[1]);
              }

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