diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py index d9ceda63d06981fdc7cf90be31646a8b0f46df94..89d6256d8bc6508117a380318835def1183c1412 100644 --- a/jass_preprocessing/__main__.py +++ b/jass_preprocessing/__main__.py @@ -11,17 +11,6 @@ import time import argparse -#| variable name | description | current default value| -#|---------------|-------------|----------------------| -#| netPath | Main project folder, must end by "/" | /mnt/atlas/ | -#| args.gwas_info* | Path to the file describing the format of the individual GWASs files | netPath+'PCMA/1._DATA/RAW.GWAS/args.gwas_info.csv' | -#| GWAS_path* | Path to the folder containing the GWASs summ stat files, must end by "/" | netPath+'PCMA/1._DATA/RAW.GWAS/'| -#| diagnostic_folder | folder for histograms of sample size distribution among SNPs | /mnt/atlas/PCMA/1._DATA/sample_size_distribution/ | -#| ldscore_format | data formated to use LDscore, 1 file per study | /mnt/atlas/PCMA/1._DATA/ldscore_data/ | -#| REF_filename* | file containing the reference panel for imputation | netPath+'PCMA/0._REF/1KGENOME/summary_genome_Filter_part2.out' | -#| pathOUT | **unused in main_preprocessing.py** | netPath+'PCMA/1._DATA/RAW.summary/'| -#| ImpG_output_Folder | main ouput folder | netPath+ 'PCMA/1._DATA/preprocessing_test/' | - def raise_duplicated_index(tag): duplicated_index = tag.duplicated() raise ValueError("'Consortium_Outcome' are duplicated for: {0}".format(duplicated_index))