Mercurial > repos > xuebing > sharplabtool

comparison tools/human_genome_variation/ldtools_wrapper.sh @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env bash
2 #
3 # Galaxy wrapper for Aakrosh Ratan's ldtools
4 #
5
6 set -e
7
8 export PATH=$PATH:$(dirname $0)
9
10 ## pagetag options
11 input=
12 rsquare=0.64
13 freq=0.00
14 sample=###
15
16 ## senatag options
17 excluded=###
18 required=###
19 output=
20
21 until [ $# -eq 0 ]
22 do
23 case $1 in
24 rsquare=*)
25 rsquare=${1#rsquare=}
26 ;;
27 freq=*)
28 freq=${1#freq=}
29 ;;
30 input=*)
31 input=${1#input=}
32 ;;
33 output=*)
34 output=${1#output=}
35 ;;
36 *)
37 if [ -z "$new_args" ]; then
38 new_args=$1
39 else
40 new_args="$new_args $1"
41 fi
42 ;;
43 esac
44
45 shift
46 done
47
48 ## run pagetag
49 pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt &> /dev/null
50 if [ $? -ne 0 ]; then
51 echo "failed: pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt"
52 exit 1
53 fi
54
55 ## run sentag
56 senatag.py neighborhood.txt snps.txt > $output 2> /dev/null
57 if [ $? -ne 0 ]; then
58 echo "failed: senatag.py neighborhood.txt snps.txt"
59 exit 1
60 fi
61
62 ## cleanup
63 rm -f snps.txt neighborhood.txt
64