Z.-L. Deng

some sequences are missing in pyfastx.Fasta object

4

I loaded a fasta file containing 4542 sequences with average length of 2.5kb, however only 4539 sequences were in the pyfastx.Fasta object. ``` fa = pyfastx.Fasta('assembly.fasta') fa['contig_4540'] # keyError ```...

Could not paste the plot generated using ggbreak into another document in Adobe illustrator

1

I created a bar plot file in PDF format using ggplot2 and ggbreak, but I could not copy and paste it in another document in Adobe illustrator (AI) because I...

Is seq-lang still being updated and maintained

2

Thank you for design such an useful programming language for the biology world. It looks amazing. The repo seems to have no new commits for more than half a year....

Thank you for developing such a great tool. It helped us to identify phenotype associated kmers. But I have a question about the way kover generating kmers. Does kover use...

Codon whl is not a supported wheel on this platform

4

Thank you for the new release. I was trying to install Codon package in Python, but it did not work on both MacOS 13 (with Intel CPU) and AlmaLinux 8.5...

https://github.com/CAMI-challenge/OPAL/blob/b30b2e4fc3edd7895e8fcb07d46f60bc9238d894/requirements/default.txt#L4 Newer version of pandas does not support Python 3.7 any longer.

cann't install roary 3.13 with mamba/conda

1

I tried to install roary with mamba but got: ``` package roary-3.13.0-pl526h516909a_0 requires perl-text-csv, but none of the providers can be installed ``` If I use conda, it will show:...

The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files

2

Since conda failed to install roary, I switched to use singularity. I pulled the image with ```shell singularity pull roary.sif docker://sangerpathogens/roary ``` But when I run the command: ```shell singularity...

ExtractionError when running taxopy on several samples in parallel with specified dmp files and keep_files=True

17

I use `taxopy` to find the LCA of taxids from a sample. ```python cd = path.dirname(path.abspath(__file__)) nodes_dmp_file = path.join(cd, "../data/nodes.dmp") names_dmp_file = path.join(cd, "../data/names.dmp") taxdb = taxopy.TaxDb(nodes_dmp=nodes_dmp_file, names_dmp=names_dmp_file, keep_files=True) ```...

remotely monitor the status of minknow protocol and run a custom script

5

Hi, Thank you developing the those useful APIs for Miniknow. I have computer A connected with Minknow and a computer B used to process the data. I am interested in...