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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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