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