Mercurial > repos > iuc > king

annotate test-data/subset_bed.sh @ 1:1932808c6fab draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
author iuc
date Mon, 18 Apr 2022 18:04:56 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
1 binary_file=ex.bed
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
2 target_markers=6000
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
3 target_cols=$(( 6 + ( $target_markers * 2 )))
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
4
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
5 dec_prefix=out
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
6 subs_prefix=sub
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
7 new_prefix="new."${target_markers}
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
8
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
9 ##conda activate plink
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
10 ## Extract binary file into new map, ped, and fam files
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
11 plink --bfile $(basename $binary_file .bed) --recode --out ${dec_prefix}
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
12
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
13 ## Subset ped and map
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
14 cat ${dec_prefix}.ped | cut -d' ' -f 1-${target_cols} > ${subs_prefix}.ped
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
15 head ${dec_prefix}.map -n ${target_markers} > ${subs_prefix}.map
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
16
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
17 ## Recode into new
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
18 plink --file ${subs_prefix} --out ${new_prefix}
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
19 echo ${new_prefix}*
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents:
diff changeset
20 ##conda deactivate