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The following has been deprecated from the BioPython repo
`from Bio.SubsMat.MatrixInfo import blosum62`
One way to fix it is to replace with
```
# from Bio.SubsMat.MatrixInfo import blosum62
from…
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import A3MIO failed.
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the…
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When running the `python setup_for_alphafold.py` script, the alignment performed by `tcrdock.sequtil.blosum_align` involves the deprecated `Bio.SubsMat` module, triggering the following warning at the…
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(Assuming that it doesn't) it would be nice if LAPIS could support returning FASTAs with "descriptions", e.g. https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta has both an accession and th…
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**Are you using the latest release?**
Funannotate 1.8.15 with all dependencies installed properly (except optional genemark), as is stated in the tutorials and documentation
**Describe the bug**
…
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After running the first code cell block we get this warning:
/usr/local/lib/python3.10/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we int…
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I have a ab1 file tracy basecall only generate 121 bases but it visualized normal after that. What's the reason tracy can not doing the basecalling after that? Thank you for help!
![7E983462-3D65-4…
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Using `docker build workflow-comparisons` on Linux Mint 21.3 with podman fails:
```
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the syst…
stain updated
23 minutes ago
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Hello,
I want to use biopython library. Probably trivial question that I am not familiar with the process.
When I run:
`!pip install biopython `
I get the following message:
```
Colle…
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Dear authors,
I tried to run the Sequeduct demo pipeline https://github.com/Edinburgh-Genome-Foundry/Sequeduct_demo/
However, at the end of the pipeline, the PDF generated only the first 2 pages, …