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I am trying to extract specific columns from a file using gawk command, but I need to do this several times.

gawk -F" " '{print $2, $7, $8, $9}' acr30R_vs_acr30NR_1.assoc.logistic >>/mnt/jw01-aruk home01/projects/jia_mtx_gwas_2016/common_files/output/imputed_dataset/all_50_mi_datasets/acr30R_vs_acr30NR_combined_coefficients/acr30nr_r_logistic_1.txt

gawk -F" " '{print $2, $7, $8, $9}' acr30R_vs_acr30NR_2.assoc.logistic >>/mnt/jw01-aruk-home01/projects/jia_mtx_gwas_2016/common_files/output/imputed_dataset/all_50_mi_datasets/acr30R_vs_acr30NR_combined_coefficients/acr30nr_r_logistic_2.txt

gawk -F" " '{print $2, $7, $8, $9}' acr30R_vs_acr30NR_3.assoc.logistic >>/mnt/jw01-aruk-home01/projects/jia_mtx_gwas_2016/common_files/output/imputed_dataset/all_50_mi_datasets/acr30R_vs_acr30NR_combined_coefficients/acr30nr_r_logistic_3.txt

The above code is to extract and print from 3 files (with suffix 1 , 2 and 3 as highlighted). I want to be able to do this for upto 50

5

You can do this with a shell loop:

for i in $(seq 1 3); do
    gawk -F" " '{print $2, $7, $8, $9}' acr30R_vs_acr30NR_${i}.assoc.logistic >>/mnt/jw01-aruk-home01/projects/jia_mtx_gwas_2016/common_files/output/imputed_dataset/all_50_mi_datasets/acr30R_vs_acr30NR_combined_coefficients/acr30nr_r_logistic_${i}.txt
done

You can replace the 1 and 3 values as appropriate in the first line. Note ${i} in the second line (in two places): these are replaced by each value in the sequence, in turn.

  • Hi Stephen, Thank you for answering this so quickly, and it is working as expected. Regards - Sam – Sam Jan 5 '17 at 10:39

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