Rhys Newell

UMAP Segmentation Faults

29

Hi, I thought it might be best to just create a new issue, for this as the issue seems a little different to https://github.com/lmcinnes/umap/issues/421 which I originally commented this error...

UMAP Intersections and unions are broken

5

Hi Leland, Just wanted to point out that fresh installs of umap seem to not be working entirely correct. The intersection and union methods seem to be the most obvious...

MUFFIN regexp to detect reads in directory

1

Hello, I'm just wondering if there is a way to change the regexp that is used to detect short reads in the input directory? Currently it is `*_R{1,2}.fastq{,.gz}` and I...

Hi Devs, Thanks for this package, really cool work and it seems very well put together. I just had a question regarding the creation of custom embedding sets. In this...

Scripts to generate usage markdown files seems to be generating wonky output, @wwood do you have any idea what might be happening and why the scripts are breaking? [recover](https://rhysnewell.github.io/rosella/usage/rosella-recover) [refine](https://rhysnewell.github.io/rosella/usage/rosella-refinel)

Nucleotide sequences of genes in 'genome_genes' directory all have identical sequences

3

Hey Joel, Hope you are doing well! Found a funky bug in the nucleotide sequence output from enrichm annotate. Here's an example: \>contig_112_pilon_1 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG \>contig_112_pilon_2 K20155 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG \>contig_112_pilon_3 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG As...

GO Annotation Vector

8

Hi @nadavbra, Cool model, I just have a few questions. The first being, did you ever recover the GO annotation vector that was lost in https://github.com/nadavbra/protein_bert/issues/6? I can't seem to...

Allow gzipped fasta files to be provided as input

1

Hey Ben, currently when providing gzipped fasta files to coverm spits out the following error: ```bash coverm genome -1 SRR16554771.downsampled.1.fastq.gz -2 SRR16554771.downsampled.2.fastq.gz -f MIC9243/PC_RaymondF_2016__P20E90__bin.24.fna.gz [2022-12-19T03:34:47Z INFO coverm] CoverM version 0.6.1...

merging v0.9.1

2

chore: merging dev branch into main

NeighborNet workflow uses circular ordering from SplitsTree4, not Huson2023, with no option to change

1

Hi SplitsTree team, This issue may be completely intentional and not an issue at all, but just wanted to flag it anyway. I've noticed that current `NeighborNet` workflow still uses...