-
Hi, thanks for developing Usher.
I'm encountering an issue. My goal is to find the 10 nearest neighbors for each sequence in a FASTA file and build a tree with input sequences + neighbors. Here's w…
-
These organism either do not have a link to Jbrowse or need Jbrowse done for them.
- [x] Acer saccharum - Transcriptome Assembly
- [x] Alnus rhombifolia - Transcriptome Assembly
- [x] Alnus rubra…
-
Could not find platform independent libraries
Could not find platform dependent libraries
Consider setting $PYTHONHOME to [:]
Fatal Python error: Py_Initialize: Unable to get the locale encoding
…
-
I wasn't able to test #1333 (which adds support for parsing complex CDSs using GenBank files) because I didn't have translated (AA) fasta files around. This made me wonder why we need the AA sequences…
-
I'm trying to use "embarrassing" parallel constructs to create a similarity matrix between two different sets of fasta files. Following is the code:
```
# -*- coding: utf-8 -*-
import sys
import …
-
Hello author,
It is impossible to create the protein embedding files because of an error while saving the file.
It seems the embeddings have different shapes and can not be saved together in a s…
-
```
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the file must be less than 65,536 characters.
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/lgs6452/.con…
-
For #2046 I am trying to remove the use of the ``Gapped`` class, and adding explicit defaulting to ``"-"`` as a gap character where necessary.
The ``to_alignment`` method tests in ``test_PhyloXML.p…
-
It is not clear, why the sequence in both objects has a different name.
This leads to a very confusing error message when creating a `SequenceEmbedding` object: `The embedding ({embedding.shape[0]})…
-
Hi,
I've been trying to resolve this deprecation by using the Bio.Align.PairwiseAligner module but have not been able to do so.
We use a python function to determine the alignment score in order t…