As a new user to Q2, I’m a bit confused by how to actually get “into” artifacts and visualizations. I even wrote a PR to the docs that was totally wrong, expecting
qiime tools view to work for both artifacts and visualizations. Shifting discussion from that PR, I wanted to ask a few questions:
Is there any reason for
viewto be separate tool commands, at least from a UX perspective? These are just pickled objects, right, so deciding which processor should be easy. Is there a reason not to combine the commands, given that you’d alias one to avoid breaking? I’d imagine wanting to view both artifact and vis.
I want to get a view of the relevant raw components of an artifact (e.g. the first few header / [qual] / sequences of a fasta/fastq, or the first few rows of a feature table). Essentially
cat sample.fastq | head. However, it seems like peek (and even the view.qiime2.org links from the tutorials) provide metadata, uuid, and provenance, but don’t actually tell me what the data is. Is there yet another viewer to do this? Is it something people aren’t doing right now? Especially since each semantic type is a first class citizen, this seems like a really necessary step for adoption.
Anyway, it looks like QIIME2 is a huge step forward and very promising. Hope to continue with it, and hope that these nit-picky points end up helping. Look forward to hearing people’s thoughts,