schorlton-bugseq

`tb-profiler update_tbdb --match_ref` fails

1

On v6.2.0, I run: `tb-profiler update_tbdb --match_ref myref.fna` I get: ``` ValueError: Command Failed: /bin/bash -c set -o pipefail; tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv --rules rules.txt --match_ref...

Hi @linsalrob and team, Thanks for the great tool! We were trying to use it on https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/033/802/525/GCF_033802525.1_ASM3380252v1/GCF_033802525.1_ASM3380252v1_genomic.gbff.gz Interestingly, we got slightly different results with PhiSpy, PhiSpy (PHROGs - used `sed...

TypeError: start=x <class 'float'>

1

Thanks for the interesting and useful tool! Hit this error on the following file, running v4.2.21 from bioconda. ```bash wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/035/013/225/GCA_035013225.1_ASM3501322v1/GCA_035013225.1_ASM3501322v1_genomic.gbff.gz gunzip GCA_035013225.1_ASM3501322v1_genomic.gbff.gz PhiSpy.py -o test --threads 2 --output_choice 4...

Hi @c0fec0de, thanks for the fantastic library! Running v`2.12.1` installed via conda/mamba and getting the following error: ```python top = Node("top", parent=None) sub0 = Node("sub0", parent=top) relaxedresolver = Resolver('name', relax=True)...

* vcfpy version: 0.13.8 * Python version: * Operating System: ### Description Thanks for the great lib! What are your thoughts in making the length in `ContigHeaderLine` an `int` if...

Thanks for the great library! Running gfapy 1.2.3 on the following file: [test.gfa.gz](https://github.com/user-attachments/files/17238218/test.gfa.gz) ```python g = gfapy.Gfa.from_file("test.gfa", vlevel=3) gfa_line = g.line("k141_11431") gfa_line.disconnect() ``` Based on the [docs](https://gfapy.readthedocs.io/en/latest/tutorial/gfa.html?highlight=disconnect#removing-lines), I expected all...

Hi, Thanks for your hard work this tool! I noticed that at least one of the rmpD alleles appears to be truncated at the first amino acid. Specifically, [rmpD_4](https://github.com/klebgenomics/Kleborate/blob/v3.1.2/kleborate/modules/klebsiella__rmst/data/rmpD.fasta#L13-L16) starts...

Thanks for your hard work on MMSeqs! I ran the following using v`17.b804f` installed via bioconda: ```bash mmseqs easy-search --search-type 2 --format-mode 1 --greedy-best-hits 1 query.fna hiv.fna result.sam tmp ```...

SAM output format @SQ headers

2

Thanks for your hard work on this tool! I noticed when using `easy-search` with v17-b804f and setting `--format-mode 1` (SAM output), the `@SQ` header lines of the SAM file are...

Custom Content Multi-Dataset Line Graph Dropping Samples?

1

### Description of bug Sorry for all of the reports and thanks for your help!! It appears that multi-dataset line graphs work when all samples are combined in a single...