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