search

hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
85 stars 26 forks source link

ModuleNotFoundError: No module named 'allel' #79

Open XiaXiaTianTian opened 2 years ago

XiaXiaTianTian commented 2 years ago

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

XiaXiaTianTian commented 2 years ago

By the way, when I just run xpclr -h. It got the same error. Maybe something wrong with installation?

yefanglee commented 2 years ago

pip install scikit-allel

hardingnj commented 2 years ago

Yes- this is an issue with packaging. Did you install via conda?

Properly updating the package installation is something I need to address here.

XiaXiaTianTian commented 2 years ago

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.

yefanglee commented 2 years ago

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.

XiaXiaTianTian commented 2 years ago

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.

yefanglee commented 2 years ago

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.

yefanglee commented 2 years ago

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.

XiaXiaTianTian commented 1 year ago

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.