Integrate a loop in a python script

Question

I am a beginner in Python and would really appreciate if someone could help me with the following: I would like to run this script 10 times and for that change for every run the sub-batch (from 0-9):

E.g. the first run would be:

python $GWAS_TOOLS/gwas_summary_imputation.py \
-by_region_file $DATA/eur_ld.bed.gz \
-gwas_file $OUTPUT/harmonized_gwas/CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz \
-parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet \
-parquet_genotype_metadata $DATA/reference_panel_1000G/variant_metadata.parquet \
-window 100000 \
-parsimony 7 \
-chromosome 1 \
-regularization 0.1 \
-frequency_filter 0.01 \
-sub_batches 10 \
-sub_batch 0 \
--standardise_dosages \
-output $OUTPUT/summary_imputation_1000G/CARDIoGRAM_C4D_CAD_ADDITIVE_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz

The second run would be

python $GWAS_TOOLS/gwas_summary_imputation.py \
-by_region_file $DATA/eur_ld.bed.gz \
-gwas_file $OUTPUT/harmonized_gwas/CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz \
-parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet \
-parquet_genotype_metadata $DATA/reference_panel_1000G/variant_metadata.parquet \
-window 100000 \
-parsimony 7 \
-chromosome 1 \
-regularization 0.1 \
-frequency_filter 0.01 \
-sub_batches 10 \
-sub_batch 1 \
--standardise_dosages \
-output $OUTPUT/summary_imputation_1000G/CARDIoGRAM_C4D_CAD_ADDITIVE_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz

I am sure this can be done with a loop but not quite sure how to do it in python?

Thank you so much for any advice, Sally

Answer 1

While we can't show you how to retrofit a loop to the python code without actually seeing the python code, you could just use a shell loop to accomplish what you want without touching the python code. For bash shell, it would look like this:

for sub_batch in {0..9}; do \
  python $GWAS_TOOLS/gwas_summary_imputation.py \
  -by_region_file $DATA/eur_ld.bed.gz \
  -gwas_file $OUTPUT/harmonized_gwas/CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz \
  -parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet \
  -parquet_genotype_metadata 
  $DATA/reference_panel_1000G/variant_metadata.parquet \
  -window 100000 \
  -parsimony 7 \
  -chromosome 1 \
  -regularization 0.1 \
  -frequency_filter 0.01 \
  -sub_batches 10 \
  -sub_batch $sub_batch \
  --standardise_dosages \
  -output $OUTPUT/summary_imputation_1000G/CARDIoGRAM_C4D_CAD_ADDITIVE_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz 
done

Answer 2

a loop in python from 0 to 10 is very easy.

for i in range(0, 10):
    do stuff