-
Much of the pipeline proceeds until seq is translating presumably detected Ig sequences. It repeatedly terminates with the "Codon 'GET' is invalid" error
pdoris$ python run_iterative_igdetective.py…
-
In working on #20, the Pythran benchmark segfaulted on me for 1e7 trees (on a machine w/32GB RAM).
Copy/paste from my terminal:
```
running
{'implementation': 'c_lib', 'sample_size': 10000000…
-
Proposal for discussion and testing to adopt f-strings, new in Python 3.6 (see python docs and PEP 498), instead of `str.format()` and decimal style string formatting. See this and subsequent comments…
-
### Setup
I am reporting a bug with Biopython 1.77, Python 3.83, and Ubuntu 18.04 as follows:
The function [Phylo.NewickIO._get_comment](https://github.com/biopython/biopython/blob/master/Bio/Ph…
-
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
We need our documentation to mention this and include an example, adding ``api_key='...'`` to an Entrez call.
…
-
**Describe the problem**
It would be great to add the large molecule fluorescent protein task introduced [here](https://arxiv.org/abs/2203.12742) as a molecular generation oracle. Code is available […
-
I have installed MultiGuideScan in a conda environment with the following dependencies installed: python==2.7.16, scikit-learn==0.16.1, coreutils, rename, biopython==1.66, pysam==0.8.3, pyfaidx==0.4.7…
-
When setting `"omit_AAs": null`, so that all possible residues can be used, an error arose from Line 25 of functions/biopython_utils.py since you cannot split an empty list. Adding a if clause like `i…
-
testdata/adeno.gb has the `order` location attribute, which we don't handle explicitly if it's different form `join`
There are more, and may be covered in the biopython, scikit-bio, and NCBI docume…
-
EUKulele stopped at the BUSCO step for me
Error message:
`BUSCO run either did not complete successfully, or returned no matches for sample`
I checked the log files and these are the outputs from…