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iprada / Circle-Map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads
MIT License
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Latest biopython version breaks Alphabet dependency #47

Open johnstonmj opened 3 years ago

johnstonmj commented 3 years ago

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?

iprada commented 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

kpkhushi15 commented 3 years ago

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 themolecule_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.

mglgc commented 1 month 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

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.

iprada commented 1 month ago

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

mglgc commented 1 month ago

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.

iprada commented 1 month ago

Ho wo do install circle-map? using biopython 1.77 should fix things.

best,

Iñigo

mglgc commented 1 month ago

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.

iprada commented 1 month ago

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

G-Thomson commented 2 weeks ago

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