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comparison tools/human_genome_variation/BEAM2_wrapper.sh @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env bash
2 #
3 # Galaxy wrapper for Yu Zhang's BEAM2 adds two new options
4 # significance=foo renames significance.txt to foo after BEAM2 is run
5 # posterior=bar renames posterior.txt to bar after BEAM2 is run
6 #
7
8 set -e
9
10 export PATH=$PATH:$(dirname $0)
11
12 ## options
13 significance=
14 posterior=
15 new_args=
16 map=
17 ped=
18
19 TFILE="/tmp/BEAM2.$$.tmp"
20
21 ## separate significance and posterior arguments from arguments to BEAM2
22 until [ $# -eq 0 ]
23 do
24 case $1 in
25 significance=*)
26 significance=${1#significance=}
27 ;;
28 posterior=*)
29 posterior=${1#posterior=}
30 ;;
31 map=*)
32 map=${1#map=}
33 ;;
34 ped=*)
35 ped=${1#ped=}
36 ;;
37 *)
38 if [ -z "$new_args" ]; then
39 new_args=$1
40 else
41 new_args="$new_args $1"
42 fi
43 ;;
44 esac
45
46 shift
47 done
48
49 ## convert input for use with BEAM2
50 lped_to_geno.pl $map $ped > $TFILE
51 if [ $? -ne 0 ]; then
52 echo "failed: lped_to_geno.pl $map $ped > $TFILE"
53 exit 1
54 fi
55
56 ## run BEAM2
57 BEAM2 $TFILE $new_args 1>/dev/null
58 if [ $? -ne 0 ]; then
59 echo "failed: BEAM2 $TFILE $new_args"
60 exit 1
61 fi
62
63 mergeSnps.pl significance.txt $TFILE
64 if [ $? -ne 0 ]; then
65 echo "failed: mergeSnps.pl significance.txt $TFILE"
66 exit 1
67 fi
68
69 ## move output files
70 mv significance.txt $significance
71 mv posterior.txt $posterior
72
73 ## cleanup
74 rm -f $TFILE
75