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gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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AttributeError: module 'Bio.Seq' has no attribute 'IUPAC' #78

Closed deoliveiralab closed 3 years ago

deoliveiralab commented 4 years ago

Version of Integron_Finder:

1.5.1

OS

Expected behavior

Output of the "integron_finder -h" command.

Actual behavior

Error message about the Bio.Seq lacking the IUPAC attribute.

Steps to reproduce behavior

[bfroliveira@bioinfomicro ~]$ integron_finder -h Traceback (most recent call last): File "/home/bfroliveira/miniconda3/bin/integron_finder", line 7, in from integron_finder.scripts.finder import main File "/home/bfroliveira/miniconda3/lib/python3.7/site-packages/integron_finder/scripts/finder.py", line 51, in from integron_finder import utils File "/home/bfroliveira/miniconda3/lib/python3.7/site-packages/integron_finder/utils.py", line 62, in read_multi_prot_fasta = make_multi_fasta_reader(Seq.IUPAC.extended_protein) AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'

I have installed using conda (I am the user of an external server) and the Biopython is updated (despite I don't know if this includes the IUPAC attribute in Bio.Seq module).

Thank you very much if you could help me with this issue.

Kind regards, Bruno Francesco.

tigerxu commented 3 years ago

Hi,

I have the same issue. Any suggestion to solve it.

Many thanks Zhuofei

jeanrjc commented 3 years ago

Hello,

We are in the process of finishing the release of version IFv2.

In the meantime, to use it, one can use a conda virtual environment, to have a clean installation of IntegronFinder v2:

conda create --name IFv2 python=3.6 
conda config --add channels bioconda # if it's not already the case
conda activate IFv2    
conda install integron_finder # install integron_finder
conda install biopython==1.72 # downgrade biopython and pandas waiting for upcoming fixes
conda install pandas=0.25.3
integron_finder ...
conda deactivate
<do something else with other version of python packages>
<come back later and anywhere>
conda activate IFv2
integron_finder ....

Within the environment, integron_finder -V should give you integron_finder version 2.0rc6

Thanks for reporting

tigerxu commented 3 years ago

Great! I have installed IFv2 using conda. Thank you very much!

bneron commented 3 years ago

fixed with last version of integron_finder on Master