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1 #! /bin/bash
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2
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3 # usage: $0 <probes file> <snps file> <probes_out> <snps_out>
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4
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5 if [ $# -ne 4 ]
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6 then
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7 echo "error, unexpected number of arguments in $0"
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8 exit
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9 fi
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10
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11 probes=$1
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12 snps=$2
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13 probes_out=$3
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14 snps_out=$4
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15
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16 echo ""
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17 echo "$0: "
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18 echo "probes: $probes, snps: $snps, probes_out: $probes_out, snps_out: $snps_out"
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19 echo ""
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20
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21 # convert probes file
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22 sed '1,1d' $probes > $probes_out.tmp
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23 sed -i "s/chr/hs/g" $probes_out.tmp
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24 sed -i '/NaN/d' $probes_out.tmp
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25 sed -i '/hsMT/d' $probes_out.tmp
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26 sed -i '/hsM/d' $probes_out.tmp
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27 cut -f1,2,3,4 $probes_out.tmp > $probes_out
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28
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29
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30 # convert snps file
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31 sed '1,1d' $snps > $snps_out
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32 sed -i "s/chr/hs/g" $snps_out
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33 sed -i '/NaN/d' $snps_out
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34 sed -i '/hsMT/d' $snps_out
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35 sed -i '/hsM/d' $snps_out
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36
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37
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38
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