francois-a
commented
2 years ago Hi, which version/repository of pgenlib are you using? I added installation instructions here.
Closed blancvccf closed 2 years ago
francois-a
commented
2 years ago Hi, which version/repository of pgenlib are you using? I added installation instructions here.
Hi I am trying to run tensorQTL and this is my code:
import pandas as pd import torch import pgenlib as pg import tensorqtl from tensorqtl import genotypeio, cis import rpy2 import rpy2.robjects as RObjects from rpy2.robjects.packages import importr qvalue = importr('qvalue', lib_loc='path')
define paths to data
plink_prefix_path = 'anotherpath' pheno = 'chr22_phenotype_nonan.bed.gz' covar = 'concatted_covar_raw.txt' prefix = 'run1_raw'
load phenotypes and covariates
phenotype_df, phenotype_pos_df = tensorqtl.read_phenotype_bed(pheno) covariates_df = pd.read_csv(covar, sep = '\t', index_col = 0).T pr = genotypeio.Plink2Reader(plink_prefix_path, verbose = True) genotype_df = pr.load_genotypes()
This is the error I receive:
Traceback (most recent call last): File "", line 1, in
File "/home/blancv/miniconda3/envs/pQTL/lib/python3.8/site-packages/tensorqtl/genotypeio.py", line 316, in load_genotypes
return pd.DataFrame(pgen.read_dosages_range(self.pgen_file, 0, self.pvar.shape[0]-1, sample_subset=sample_idxs),
File "/home/blancv/miniconda3/envs/pQTL/lib/python3.8/site-packages/tensorqtl/pgen.py", line 106, in read_dosages_range
with pg.PgenReader(pgen_path.encode(), sample_subset=sample_subset) as r:
AttributeError: module 'pgenlib' has no attribute 'PgenReader'
The error occurs on the last line (where I call load_genotypes)
I have installed pgenlib so I am not sure what to do here. Thanks for the help