Antônio Camargo

Hey Rob! The *Escherichia coli* K12 genome seems to be missing more than one prophage. Here's one that I curated manually: ``` contig gene start end --------------------------------------------------------------- NC_000913 RAST2:fig|83333.998.peg.2428 2464528...

Noisy perceptual derivatives

2

I'm playing around with viscm and I noticed that all colormaps that I create end up with very noisy perceptual derivatives:  [test_cm.jscm.txt](https://github.com/matplotlib/viscm/files/13061531/test_cm.jscm.txt) This is not a problem with the...

Kernel won't start in local notebooks

2

I'm testing the extension in my local machines (VSCode 1.61.2, macOS 11.6 / elementary OS 6) and it seems the kernel won't start. I can get any code to run...

Invalid pointer during calculation of alignments

1

Version: `commit 3eabfaff83bb77eac5ef342e8905cc4f7d378cb7` Command: ``` ./conterminator/build/bin/conterminator protein GTDB97.faa taxonomy/mapping_new conterminator_phylum_level conterminator_tmp --threads 64 --ncbi-tax-dump taxonomy --kingdoms 3,9,22,28,71,85,104,113,188,435,558,600,661,798,948,2112,2179,2185,2197,2222,2231,2290,2346,2367,2457,2526,2599,2662,2804,2844,2936,2947,3026,3093,3196,3236,3259,3295,3332,3478,3486,3519,3588,3721,3764,3806,3852,3869,3971,4049,4123,4138,4295,4380,4393,4426,4438,4480,4574,4637,4747,4807,4962,5058,5211,5295,5301,5341,5428,5455,5610,5785,5850,5876,6053,6077,6352,6994,7152,7497,7678,7997,8069,8163,8265,8415,8508,9033,9459,9518,9602,9620,9659,9816,9982,10092,10112,10373,10409,10624,10701,10941,10980,11478,12122,12426,12439,12474,12788,12916,13990,14290,14512,14627,14692,14712,14955,15712,16418,16488,17029,17211,17233,17428,17878,17918,18303,18551,19564,19757,19952,20114,20624,21463,22205,22539,22684,23843,24111,24497,26693,27254,29002,29170,30513,31392,32011,33650,34643,34865,35143 ``` Output: ``` Tmp conterminator_tmp folder does not exist or is not a...

Include archaeal plasmids

2

PLSDB currently hosts only bacterial plasmids. WOuld it be within the project's scope to also add plasmids of Archaea?

feat: `eza` is substantially slower than `ls` in large directories

16

As discussed [here](https://github.com/orgs/eza-community/discussions/816), `eza` is significantly slower than `ls` when listing files in large directories. This issue persists with the latest version (0.18.9). Here's a benchmark for a directory with...

When I try to reverse search images from some sites (like Facebook), I get this error: "The URL doesn't refer to an image or the image is not publicly accessible."...

Add RabbitTClust to Bioconda

8

Hi @XiaomingXu1995 First, I'd like to congratulate you for RabbitTClust. I spent weeks trying to find a clustering algorithm that worked in the scale I needed and RabbitTClust solved all...

The example notebook show the utilization of a Greengenes-style lineage as a prompt for generation. However, it does not address the process of prompting for non-chromosomal sequences. For viruses, was...

## Expected Behavior In circular sequences, the last and the first gene in the sequences are neighbors and should be treated as so when searching gene clusters. ## Current Behavior...