Mercurial > repos > dereeper > sniplay
annotate ped2bed/ped2bed.sh @ 12:88748d846a20 draft
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
| author | dereeper |
|---|---|
| date | Tue, 14 Aug 2018 08:21:55 -0400 |
| parents | 420b57c3c185 |
| children |
| rev | line source |
|---|---|
| 1 | 1 #!/bin/bash |
| 2 ped=$1 | |
| 3 map=$2 | |
| 4 bed=$3 | |
| 5 fam=$4 | |
| 6 bim=$5 | |
| 7 logs=$6 | |
| 8 | |
| 9 directory=`dirname $0` | |
| 10 mkdir tmpdir$$ | |
| 11 cp -rf $ped tmpdir$$/input.ped | |
| 12 cp -rf $map tmpdir$$/input.map | |
| 13 | |
| 14 plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1 | |
| 15 | |
| 16 mv tmpdir$$/out.bed $bed | |
| 17 mv tmpdir$$/out.fam $fam | |
| 18 mv tmpdir$$/out.bim $bim | |
| 19 | |
| 20 |