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. :)
> 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.
Big 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.
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:
versus BioPython: 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/