Koeng101
Koeng101
### Overview `opentrons_simulate` on python3.11 does not work due to coroutines being updated. ### Steps to reproduce - Install python3.11 - Install opentrons (`pip install opentrons`) - Run `opentrons_simulate` ###...
Why is both poetry and pip used? Shouldn't dependencies be handled by poetry, then after `poetry install` run with `poetry run python main.py`? When I do try that, I get...
https://github.com/Koeng101/dnadesign/blob/85e882045b7cd1e61284431e5e3b8985243f1fbd/lib/synthesis/codon/codon.go#L264C1-L267C5 ```go for _, feature := range sequence.Features { if feature.Type == "CDS" { if _, ok := feature.Attributes["pseudo"]; ok { continue } seq, _ := feature.GetSequence() codingRegionsBuilder.WriteString(seq) genes++ }...
My dream for DnaDesign is to integrate AI systems for designing DNA - the other API request is a means to this end. However, I want the end-to-end pipeline to...
vcf turns out to help with some of my sequencing. I like having pileup as a backup, though, for manual viewing. Generating vcf with bcftools is a good way to...
`seq_recovery=0.4152_0` for example, cannot be processed into a megamash table because it doesn't have any unique 16mers. This is because of a flawed assumption: ESPECIALLY in protein variant libraries, 16mer...
Api
API adds an OpenAPI interface to DnaDesign. This allows other programs to work with DnaDesign. In particular, we have a focus on supporting an embedded lua environment and python interactivity....
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200061/ We mapped the sequencing reads to the dual-barcode sequences with 56 bp in length using Minimap2 (v2.11) [[26](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200061/#R26)] by -k7 -A1 -m42 -w1 options.
I merged much of linearfold directly from https://github.com/allyourbasepair/rbscalculator - and so, not only are the linters *very* unhappy, but there are lots of missing spots for better documentation (though vivek...
Referencing https://github.com/bebop/poly/issues/434 @carreter is asking for a full rewrite there, but I think I disagree. Useful link to the [spec](https://www.ncbi.nlm.nih.gov/genbank/release/current/). - Feature.GetSequence() always returns a nil error value [link](https://github.com/bebop/poly/issues/352) This...