Closed Benedict-Carling closed 11 months ago
Thanks for bringing attention to this, I'll have a look.
So will it eventually be merged?
@antonkulaga yes, certainly. I was tied up in another project recently published among other things, but now can work on this.
Hi there, I also ran into this UndefinedSequenceError
issue with plotting gff
files that were working in the past.
Note: The test gff
file in the PR includes embedded ##FASTA
sequence. In my experience that is rather rare, and my particular gff
file doesn't include it
I've been installing dna_feature_viewer
from conda/mamba . If this PR cannot be merged, I presume it should also be possible to mark dna_feature_viewer
v3.12
as only compatible with biopython <=1.8.0 in pip/conda so that incompatible environments aren't made. From my troubleshooting, this is a past conda
environment that worked:
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- jupyterlab
- matplotlib
- bcbio-gff=0.6.9=pyh5e36f6f_0
- biopython=1.80=py310h5764c6d_0
- bx-python=0.9.0=py310hdacdf33_0
- dna_features_viewer=3.1.2=pyh7cba7a3_0
This is a current conda
environment that does not work. Note that bcbio-gff
and bx-python
were also updated, but the root cause clearly seems to be the updated biopython
.
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- jupyterlab
- matplotlib
- bcbio-gff=0.7.0=pyh7cba7a3_0
- biopython=1.81=py310h2372a71_1
- bx-python=0.10.0=py310h551a815_0
- dna_features_viewer=3.1.2=pyh7cba7a3_0
Hello,
I'm excited to contribute to this repository! I've cloned the repository and ran the tests. I noticed that the
test_gff
is currently broken when using the latest version of Biopython.In the latest Biopython version (1.81),
UnknownSeq
has been depreciated. As a result, attempts to access the sequence of unknown sequences now throw an error calledUndefinedSequenceError
.To address this issue, I suggest adding a check to verify if the sequence is defined before attempting to access its content. By doing this, we can avoid the
UndefinedSequenceError
and proceed with a value ofNone
in such cases.I've also included an additional test for a GFF file with a known sequence to ensure that sequences are correctly passed through when they are provided.
I'm eager to hear your thoughts on this. Please let me know if there's anything else I need to do.
Best regards, Ben