Open johnstonmj opened 3 years ago
Hi John!
Thanks for reporting! and thanks for solving it. I am very busy right now, and you have made my life easier. This are the best type of issues I can get. I will update the bioconda recipe tomorrow.
Best,
Iñigo
I encountered the error:
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
molecule_typeas an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information
This seems to have changed with biopython 1.78 Installing biopython=1.77 fixed this issue for me.
Perhaps update the conda recipe to specify biopython=1.77?
Hi John! I encountered the same issue. After seeing your post I changed the biopython version==1.77 and now error got fixed. I am able to run the commands successfully.
Thankx for posting this issue.
Hi John!
Thanks for reporting! and thanks for solving it. I am very busy right now, and you have made my life easier. This are the best type of issues I can get. I will update the bioconda recipe tomorrow.
Best,
Iñigo
Hi, Actually, the code is not fixed to date. I had to remove the importing Bio.Alphabet module line from simulations.py script in order to fix the issue. Cheers.
Hi,
Based on the commit https://github.com/iprada/Circle-Map/commit/20d52b5533d67e8aab397f418d6e06e9a0d13b0f this was handled as it ensures that biopython 1.77 is used. Which version of biopython are you using?
best,
Iñigo
Hi,
Based on the commit 20d52b5 this was handled as it ensures that biopython 1.77 is used. Which version of biopython are you using?
best,
Iñigo
Hi Iñigo, The biopython 1.84 version.
Cheers.
Ho wo do install circle-map? using biopython 1.77 should fix things.
best,
Iñigo
Ho wo do install circle-map? using biopython 1.77 should fix things.
best,
Iñigo
Using conda as described in the Code Installation section: conda install -c bioconda circle-map
Best.
I think the the setup.py should take care of installing biopython 1.77 but I might be wrong. Downgrading to 1.77 should do the job for you
For some reason it looks like the version number on bioconda was not updated when the version of biopython was set to 1.77 (https://anaconda.org/bioconda/circle-map/files). So when you don't specify the build the older version gets installed.
Try conda install -c bioconda circle-map=1.1.4=pyh5e36f6f_2
I encountered the error:
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 ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information
This seems to have changed with biopython 1.78 Installing biopython=1.77 fixed this issue for me.
Perhaps update the conda recipe to specify biopython=1.77?