I selected one of the files under the WES plink format folder, and clicked copy path. Example below:
path_to_family_file = '/project-{string of letters which is the project ID}:/Bulk/Exome sequences_Previous exome releases/Population level exome OQFE variants, PLINK format - interim 200k release/'
plink_fam_df = pd.read_csv(path_to_family_file, delimiter='\s', dtype='object',
names = ['FID','IID','Father ID','Mother ID', 'sex', 'Pheno'], engine='python')
I keep getting an error that the file or directory doesn't exist. I am confused about how to get the correct path to these files.
?
The scripts (partB-G) assume that you are running them from a LOCAL command line and not from within a jupyter notebook. Once the phenotype/covariate file is created and saved back to the project, you can end that notebook and move to the scripts.
The path should be "/mnt/project/" without the project id information. by logging in with the dx login command, and selecting a project with dx select, you already have access to the files linked to the "-{string of letters which is the project ID}".
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Thank you!
The scripts (partB-G) assume that you are running them from a LOCAL command line and not from within a jupyter notebook. Once the phenotype/covariate file is created and saved back to the project, you can end that notebook and move to the scripts.
The path should be "/mnt/project/" without the project id information. by logging in with the dx login command, and selecting a project with dx select, you already have access to the files linked to the "-{string of letters which is the project ID}".
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