braker2遇到biopython报错

在运行braker2的时候遇到了报错

/home/lx_sky6/software/miniconda3/envs/braker2/bin/python3 /home/lx_sky6/software/miniconda3/envs/braker2/bin/getAnnoFastaFromJoingenes.py

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](https://link.zhihu.com/?target=https%3A//links.jianshu.com/go%3Fto%3Dhttps%253A%252F%252Fbiopython.org%252Fwiki%252FAlphabet) for more information.

image.png

查看一下安装的biopython版本

$python
>>> import Bio
>>> print(Bio.__version__)
1.80

由于1.80的版本已经删掉了Alphabet 模块

先删掉当前版本的biopython
在安装1.76版本的biopython

pip3 install biopython==1.76

再次运行

/home/lx_sky6/software/miniconda3/envs/braker2/bin/python3 /home/lx_sky6/software/miniconda3/envs/braker2/bin/getAnnoFastaFromJoingenes.py
usage: getAnnoFastaFromJoingenes.py [-h] -g GENOME -o OUT
                                    [-t TRANSLATION_TABLE] [-s FILTER] [-p]
                                    (-f GTF | -3 GFF3)
getAnnoFastaFromJoingenes.py: error: the following arguments are required: -g/--genome, -o/--out