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1 #!/bin/bash
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2
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3
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4 tool_path=$(dirname $0)
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5
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6 filein=$1
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7 fileout_label=$(date "+%Y%m%d%H%M%S")
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8 fileout=$2
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9 filelog=$3
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10 frequency=$4
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11 max_freq=$5
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12 allow_missing=$6
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13 type=${7}
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14 bound_start=${8}
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15 bound_end=${9}
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16
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17 cp -rf $filein input$$.vcf
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18
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19 if [ "${10}" != "None" ]
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20 then samples="--samples ${10}"
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21 fi
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22
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23 if [ "${11}" != "None" ]
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24 then chromosomes="--chromosomes ${11}"
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25 fi
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26
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27 if [ "$bound_start" -gt "$bound_end" ]
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28 then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
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29 fi
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30
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31
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32 export="VCF"
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33
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34 perl $tool_path/Plink.pl --input input$$.vcf --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --type $type --bounds $bound_start','$bound_end $samples $chromosomes
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35
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36
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37 #echo ${16} >>$fileout_label.log
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38 #echo ${15} >>$fileout_label.log
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39 #echo ${17} >>$fileout_label.log
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40 #echo ${18} >>$fileout_label.log
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41
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42 if [ "$export" = "VCF" ]
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43 then cp $fileout_label.vcf $fileout ; rm $fileout_label.vcf
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44 else cp $fileout_label.bed $fileout; cp $fileout_label.bed ${15} ; cp $fileout_label.bim ${18} ;rm $fileout_label.bed $fileout_label.fam $fileout_label.bim
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45 fi
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46
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47 cp $fileout_label.log $filelog
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48 rm $fileout_label.log
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49
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