bioperl-live

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

Experiments aren't usually written in FORTRAN. The programmer is by far the slowest part of HPC. It often makes sense to use the language you're fastest at instead of the language that will run the fastest. It's very common for experiments to be written in languages not know for their performance (Java, Matlab, Perl, and Python for instance). For reference, here are some of the packages commonly used in experiments[1]: BLAS Fortran http://www.netlib.org/blas/#_software NCBI BLAST C++ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.30+-src.zip BFAST C http://sourceforge.net/projects/bfast/ BioPerl Perl https://github.com/bioperl/bioperl-live Bowtie C++, C http://sourceforge.net/p

I'm a bit surprised at the implied superiority to the other Bio* projects. None of them started as a copy of BioPerl (and btw, it's "Biopython", not "BioPython"), and none of them are trying to implement all of the features of BioPerl. For that matter, the other projects implement features that BioPerl doesn't have. It's interesting that the example supports a comment in the FASTA record. I wonder why the author included it. I've never seen a comment used in the wild, but then again I haven't worked with FASTA files for some time. My experience was that nearly every tool would break if you give it a FASTA file with a comment. For example, the BioPerl FASTA parser is at https://github.com/bioperl/bioperl-live/blob/master/Bio/SeqI... , where you can see it doesn't support a comment. Since the chance of breakage is so high, my belief 10 year

One point of evidence can be the BioPerl and BioPython communities. On github there are currently 111 stars and 57 forks for BioPerl while there are 350 stars and 179 forks for BioPython. BioPerl: https://github.com/bioperl/bioperl-live BioPython: https://github.com/biopython/biopython