xpclr
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hardingnj
ModuleNotFoundError: No module named 'allel'
Dear all, I am trying xpclr installed by conda but got the following error. I tried diffrent vcf still got this.
Traceback (most recent call last): File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/bin/xpclr", line 4, in <module> __import__('pkg_resources').run_script('xpclr==1.1.2', 'xpclr') File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/lib/python3.6/site-packages/pkg_resources/__init__.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1445, in run_script exec(script_code, namespace, namespace) File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/lib/python3.6/site-packages/xpclr-1.1.2-py3.6.egg/EGG-INFO/scripts/xpclr", line 5, in <module> File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/lib/python3.6/site-packages/xpclr-1.1.2-py3.6.egg/xpclr/__init__.py", line 3, in <module> File "/ds3200_1/users_root/xia/.pyenv/versions/3.6.5/lib/python3.6/site-packages/xpclr-1.1.2-py3.6.egg/xpclr/methods.py", line 8, in <module> ModuleNotFoundError: No module named 'allel'
I followed this command,
xpclr --format vcf --input 108.filtered.exInDe.biallelic.maf.rm_mis.ld.vcf.gz --samplesA m --samplesB e --chr LG01 --minsnps 100 --size 50000 --step 5000 --out m_e.LG01
Is it due to that this version xpclr does not support this format?
Thanks for your help. Xia
By the way, when I just run xpclr -h. It got the same error.
Maybe something wrong with installation?
Yes- this is an issue with packaging. Did you install via conda?
Properly updating the package installation is something I need to address here.
pip install scikit-allelis temporarily is unavailable for my system.
I can only used conda to install it now. conda create -n xpclr python=3.10.4 xpclr=1.1.2
Do I need to reinstall this? But currently the newest version is v1.1.2.
did you run it correctly? I have installed xpclr with python and conda, but not worked. So I changed the original version and it works.
did you run it correctly? I have installed xpclr with python and conda, but not worked. So I changed the original version and it works.
Not yet. Neither the original version XPCLR.
did you run it correctly? I have installed xpclr with python and conda, but not worked. So I changed the original version and it works.
Not yet. Neither the original version XPCLR.
what's your software errors? do not use vcf files, change it to geno and snp files.
sorry, I forgot the process with my package. I used " python setup.py install", python >3. Input files are geno and snp, vcf does not work.
sorry, I forgot the process with my package. I used " python setup.py install", python >3. Input files are geno and snp, vcf does not work.
It is OK. Now I have solved this. Installed it by conda. And then used it in absolute path. And it can work with vcf well. Than you all.