I am using the OBITools3 to try to analyze DNA metabarcoding data. I have had the same error come up multiple times when trying to run obi commands, such as obi taxonomy or obi alignpairedend. My code appears to be formatted correctly, and I don't know why I am getting the error! I'm using OBITools through a server at my university. I installed The OBITools 3 - Version 3.0.1b22 in a v-env with Python 3.6.8.
Here is the code I used to install OBItools
python3 -m venv new-env
source new-env/bin/activate
pip install --upgrade pip setuptools wheel Cython
pip install OBITools3
The code I tried to run:
obi alignpairedend --only 20 /data/student/td/R1.fastq -R /data/student/td/R2.fastq /data/student/td/OBIToolsTesting/ObiAligned.fastq
And the error info:
Traceback (most recent call last):
File "/home/td/new-env/bin/obi", line 62, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/alignpairedend.pyx", line 133, in obitools3.commands.alignpairedend.run
File "python/obitools3/uri/decode.pyx", line 177, in obitools3.uri.decode.open_uri
AttributeError: 'str' object has no attribute 'isascii'
I don't know much about Python, or virtual environments, and I can't figure out what the issue is, so any help is greatly appreciated! Would this be a version issue?
isascii()method of strings was added in Python 3.7, so it's not available to you with your current version.