annotate ped2bed/ped2bed.sh @ 3:345f88a8f483 draft

Uploaded
author dereeper
date Fri, 10 Jul 2015 10:38:43 -0400
parents 420b57c3c185
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
1 #!/bin/bash
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
2 ped=$1
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
3 map=$2
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
4 bed=$3
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
5 fam=$4
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
6 bim=$5
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
7 logs=$6
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
8
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
9 directory=`dirname $0`
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
10 mkdir tmpdir$$
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
11 cp -rf $ped tmpdir$$/input.ped
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
12 cp -rf $map tmpdir$$/input.map
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
13
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
14 plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
15
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
16 mv tmpdir$$/out.bed $bed
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
17 mv tmpdir$$/out.fam $fam
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
18 mv tmpdir$$/out.bim $bim
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
19
420b57c3c185 Uploaded
dereeper
parents:
diff changeset
20