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It's an impressive project, but I'm not sure the niche is big enough. It's certainly come a long way since the last time I looked at it! My biggest concern is
by fwip 5y ago
It's an impressive project, but I'm not sure the niche is big enough. It's certainly come a long way since the last time I looked at it!
My biggest concern is that Seq sucks users into a sort of local maximum. While piping syntax is nice, and the built-in routines are handy, it's a lot less flexible than a "mainstream" programming language, simply because of the smaller community and relative paucity of libraries. BioPython[1] has been around a long long time, and I think a lot of potential users of Seq would be better suited by using a regular bioinformatics library in the language they know best.
e.g: The example of reading Fasta files in Seq:
# iterate over everything
for r in FASTA('genome.fa'):
print r.name
print r.seq
versus BioPython:
from Bio import SeqIO
for r in SeqIO.parse("genome.fa", "fasta"):
print(r.id)
print(r.seq)
It might be pretty useful as a teaching tool, but I'm skeptical of its long-term benefit to professionals. I'm not sure the ecosystem of Seq users will be large enough, y'know? Again, it's pretty impressive work, and it's come a long way. I wish the devs all the best. :)
1. https://biopython.org/ https://biopython.org/
- chmaynard 5y ago> It's an impressive project, but I'm not sure the niche is big enough. Big enough for what? Instead of a gratuitous critique of its "benefit to professionals", maybe you could comment on the project's design choices and implementation. That would be more useful to us amateurs.
- ivirshup 5y agoBig enough to attract developers. As a bioinformatic tool developer, I'm probably gonna stick with Python and Julia since I have access to wider ecosystem of general purpose mathematical libraries and expertise.
- fwip 5y agoYeah, basically this. A big enough niche to have enough users to survive as a language, and to be worth recommending to colleagues.