Mercurial > repos > iuc > king
comparison test-data/subset_bed.sh @ 1:9256ad8b3fd3 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
| author | iuc |
|---|---|
| date | Mon, 18 Apr 2022 18:04:24 +0000 |
| parents | |
| children |
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| 0:1ca080fd3a48 | 1:9256ad8b3fd3 |
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| 1 binary_file=ex.bed | |
| 2 target_markers=6000 | |
| 3 target_cols=$(( 6 + ( $target_markers * 2 ))) | |
| 4 | |
| 5 dec_prefix=out | |
| 6 subs_prefix=sub | |
| 7 new_prefix="new."${target_markers} | |
| 8 | |
| 9 ##conda activate plink | |
| 10 ## Extract binary file into new map, ped, and fam files | |
| 11 plink --bfile $(basename $binary_file .bed) --recode --out ${dec_prefix} | |
| 12 | |
| 13 ## Subset ped and map | |
| 14 cat ${dec_prefix}.ped | cut -d' ' -f 1-${target_cols} > ${subs_prefix}.ped | |
| 15 head ${dec_prefix}.map -n ${target_markers} > ${subs_prefix}.map | |
| 16 | |
| 17 ## Recode into new | |
| 18 plink --file ${subs_prefix} --out ${new_prefix} | |
| 19 echo ${new_prefix}* | |
| 20 ##conda deactivate |