Koeng101

Failure → spec/loader/loader_spec.lua @ 7: tl.loader on .tl files reports filename correctly in debug info

3

On a fresh git clone, I tried the following test: ``` luarocks test tl dev-1 depends on dkjson (2.6-1 installed) ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●◌●●●●●●●●●●●●●●●●●●●●●●●●●●●●◌●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●◼●●●●●●●●●●●◌●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●◌●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●◌●●●●●●◌●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 931 successes / 1 failure / 0 errors /...

Default codon tables

6

We should add default codon tables of the following organisms: 1. Escherichia coli MG1655 2. Bacillus subtilis 168 3. Vibrio natriegens (whatever type strain) 4. Saccharomyces cerevisiae BY4741/BY4742 (used for...

**Is your feature request related to a problem? Please describe.** Codon tables should have start codon statistics available for use.

When developing, it makes more sense for GbkLocationString to be a feature attribute, since location is entirely derived from it.

Why is there Linear and Circular bools on Locus struct?

4

**Describe the bug** In io.go at line 80 + 81, there is a `Circular` and `Linear` field, both as booleans. Couldn't you just have one? (Since if Circular is false,...

Poly does not faithfully keep label names the same

3

**Describe the bug** In `puc19.gbk`the first primer is named `/label="M13/pUC Reverse"`. If read through Poly, this gets changed to `/label="M13pUC Reverse"` **Expected behavior** The labels should be the same.

BtgZI fasta fails parsing

3

**Describe the bug** http://rebase.neb.com/cgi-bin/seqsget?BtgZI.NEBC8843.pro parses using the build in parser, but spaces are not removed. We should remove all spaces in the fasta parsers. **To Reproduce** Download the linked fasta...

Gff fails to parse on basic Gff file

3

```go package main import ( "fmt" "github.com/koeng101/poly" ) // Started at 4:44 // 5:00 finished downloading all files // 5:07 discovered big bug with gb file parsing (give this to...

Seqhash with overhangs

2

Seqhash cannot represent DNA with overhangs or other DNA that are bound without perfect matches. In actual experimentation, this kind of structure is often found, and should be addressed. We...

**Describe the bug** Having default stochastic codon optimization is annoying. There should be a way to add a seed to get consistent randomization. **Expected behavior** Add the ability to seed...