Skip to content

Change delimiter in CSV read from delim_whitespace to sep #23

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
SamueleSoraggi wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Change delimiter in CSV read from delim_whitespace to sep #23

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions pops.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -91,14 +91,14 @@ def get_indices_in_target_order(ref_list, target_names):
### --------------------------------- READING DATA --------------------------------- ###

def read_gene_annot_df(gene_annot_path):
gene_annot_df = pd.read_csv(gene_annot_path, delim_whitespace=True).set_index("ENSGID")
gene_annot_df = pd.read_csv(gene_annot_path, sep='\s+').set_index("ENSGID")
gene_annot_df["CHR"] = gene_annot_df["CHR"].astype(str)
return gene_annot_df


def read_magma(magma_prefix, use_magma_covariates, use_magma_error_cov):
### Get Y and Y_ids
magma_df = pd.read_csv(magma_prefix + ".genes.out", delim_whitespace=True)
magma_df = pd.read_csv(magma_prefix + ".genes.out", sep='\s+')
Y = magma_df.ZSTAT.values
Y_ids = magma_df.GENE.values
if use_magma_covariates is not None or use_magma_error_cov is not None:
Expand Down